diff --git a/charon/cmd/command.py b/charon/cmd/command.py
index 8e197675..a4a87397 100644
--- a/charon/cmd/command.py
+++ b/charon/cmd/command.py
@@ -104,7 +104,7 @@ def upload(
     version: str,
     target: str,
     root_path="maven-repository",
-    ignore_patterns=None,
+    ignore_patterns: List[str] = None,
     debug=False,
     quiet=False,
     dryrun=False
@@ -128,6 +128,7 @@ def upload(
     archive_path = __get_local_repo(repo)
     npm_archive_type = detect_npm_archive(archive_path)
     product_key = f"{product}-{version}"
+    prefix_ = conf.get_bucket_prefix(target)
     if npm_archive_type != NpmArchiveType.NOT_NPM:
         logger.info("This is a npm archive")
         handle_npm_uploading(archive_path, product_key,
@@ -144,6 +145,7 @@ def upload(
                                ignore_patterns_list,
                                root=root_path,
                                bucket_name=aws_bucket,
+                               prefix=prefix_,
                                dry_run=dryrun)
 
 
@@ -221,7 +223,7 @@ def delete(
     version: str,
     target: str,
     root_path="maven-repository",
-    ignore_patterns=None,
+    ignore_patterns: List[str] = None,
     debug=False,
     quiet=False,
     dryrun=False
@@ -245,6 +247,7 @@ def delete(
     archive_path = __get_local_repo(repo)
     npm_archive_type = detect_npm_archive(archive_path)
     product_key = f"{product}-{version}"
+    prefix_ = conf.get_bucket_prefix(target)
     if npm_archive_type != NpmArchiveType.NOT_NPM:
         logger.info("This is a npm archive")
         handle_npm_del(archive_path, product_key,
@@ -261,6 +264,7 @@ def delete(
                          ignore_patterns_list,
                          root=root_path,
                          bucket_name=aws_bucket,
+                         prefix=prefix_,
                          dry_run=dryrun)
 
 
diff --git a/charon/config.py b/charon/config.py
index 2010bc7f..db28c970 100644
--- a/charon/config.py
+++ b/charon/config.py
@@ -19,6 +19,8 @@
 import os
 import logging
 
+from charon.utils.strings import remove_prefix
+
 CONFIG_FILE = "charon.yaml"
 
 logger = logging.getLogger(__name__)
@@ -62,8 +64,8 @@ def get_bucket_prefix(self, target: str) -> str:
                            "in charon configuration, so no prefix will "
                            "be used", target)
             prefix = ""
-        if prefix.startswith("/"):
-            prefix = prefix[1:]
+        # removing first slash as it is not needed.
+        prefix = remove_prefix(prefix, "/")
         return prefix
 
 
diff --git a/charon/pkgs/indexing.py b/charon/pkgs/indexing.py
index 447904f8..693db242 100644
--- a/charon/pkgs/indexing.py
+++ b/charon/pkgs/indexing.py
@@ -21,6 +21,8 @@
 import logging
 from typing import List, Set
 
+from charon.utils.strings import remove_prefix
+
 logger = logging.getLogger(__name__)
 
 
@@ -50,7 +52,11 @@ def generate_index_file_content(self) -> str:
 
 
 def generate_indexes(
-    top_level: str, changed_dirs: List[str], s3_client: S3Client, bucket: str
+    top_level: str,
+    changed_dirs: List[str],
+    s3_client: S3Client,
+    bucket: str,
+    prefix: str
 ) -> List[str]:
     if top_level[-1] != '/':
         top_level += '/'
@@ -70,13 +76,13 @@ def generate_indexes(
     s3_folders = sorted(s3_folders, key=FolderLenCompareKey)
     for folder_ in s3_folders:
         index_html = __generate_index_html(
-            s3_client, bucket, folder_, top_level
+            s3_client, bucket, folder_, top_level, prefix
         )
         if index_html:
             generated_htmls.append(index_html)
 
     root_index = __generate_index_html(
-        s3_client, bucket, "/", top_level
+        s3_client, bucket, "/", top_level, prefix
     )
     if root_index:
         generated_htmls.append(root_index)
@@ -88,11 +94,16 @@ def __generate_index_html(
     s3_client: S3Client,
     bucket: str,
     folder_: str,
-    top_level: str
+    top_level: str,
+    prefix: str = None
 ) -> str:
+    if folder_ != "/":
+        search_folder = os.path.join(prefix, folder_) if prefix else folder_
+    else:
+        search_folder = prefix if prefix else "/"
     contents = s3_client.list_folder_content(
         bucket_name=bucket,
-        folder=folder_
+        folder=search_folder
     )
     index = None
     if len(contents) == 1 and contents[0].endswith("index.html"):
@@ -106,10 +117,22 @@ def __generate_index_html(
             file_paths=[removed_index],
             bucket_name=bucket,
             product=None,
-            root=top_level
+            root=top_level,
+            key_prefix=prefix
         )
     elif len(contents) >= 1:
-        index = __to_html(contents, folder_, top_level)
+        real_contents = []
+        if prefix and prefix.strip() != "":
+            for c in contents:
+                if c.startswith(prefix):
+                    real_c = remove_prefix(c, prefix)
+                    real_c = remove_prefix(real_c, "/")
+                    real_contents.append(real_c)
+                else:
+                    real_contents.append(c)
+        else:
+            real_contents = contents
+        index = __to_html(real_contents, folder_, top_level)
 
     return index
 
@@ -119,6 +142,7 @@ def __to_html(contents: List[str], folder: str, top_level: str) -> str:
     if folder != "/":
         items.append("../")
         for c in contents:
+            # index.html does not need to be included in html content.
             if not c.endswith("index.html"):
                 items.append(c[len(folder):])
     else:
diff --git a/charon/pkgs/maven.py b/charon/pkgs/maven.py
index bcec8f47..c7857e75 100644
--- a/charon/pkgs/maven.py
+++ b/charon/pkgs/maven.py
@@ -16,6 +16,7 @@
 import charon.pkgs.indexing as indexing
 from charon.utils.files import write_file
 from charon.utils.archive import extract_zip_all
+from charon.utils.strings import remove_prefix
 from charon.storage import S3Client
 from charon.pkgs.pkg_utils import upload_post_process, rollback_post_process
 from charon.config import get_template
@@ -181,6 +182,7 @@ def handle_maven_uploading(
     ignore_patterns=None,
     root="maven-repository",
     bucket_name=None,
+    prefix=None,
     dir_=None,
     do_index=True,
     dry_run=False
@@ -221,18 +223,24 @@ def handle_maven_uploading(
         _handle_error(err_msgs)
         # Question: should we exit here?
 
+    prefix_ = remove_prefix(prefix, "/")
     # 4. Do uploading
     logger.info("Start uploading files to s3")
     s3_client = S3Client(dry_run=dry_run)
     bucket = bucket_name
-    (_, failed_files) = s3_client.upload_files(
-        file_paths=valid_mvn_paths, bucket_name=bucket, product=prod_key, root=top_level
+    _, failed_files = s3_client.upload_files(
+        file_paths=valid_mvn_paths, bucket_name=bucket,
+        product=prod_key, root=top_level, key_prefix=prefix_
     )
     logger.info("Files uploading done\n")
 
     # 5. Use uploaded poms to scan s3 for metadata refreshment
     logger.info("Start generating maven-metadata.xml files for all artifacts")
-    meta_files = _generate_metadatas(s3_client, bucket, valid_poms, top_level)
+    meta_files = _generate_metadatas(
+        s3=s3_client, bucket=bucket,
+        poms=valid_poms, root=top_level,
+        prefix=prefix_
+    )
     logger.info("maven-metadata.xml files generation done\n")
 
     failed_metas = meta_files.get(META_FILE_FAILED, [])
@@ -243,7 +251,8 @@ def handle_maven_uploading(
             meta_file_paths=meta_files[META_FILE_GEN_KEY],
             bucket_name=bucket,
             product=prod_key,
-            root=top_level
+            root=top_level,
+            key_prefix=prefix_
         )
         failed_metas.extend(_failed_metas)
         logger.info("maven-metadata.xml updating done\n")
@@ -252,14 +261,18 @@ def handle_maven_uploading(
     # index is similar to metadata, it will be overwritten everytime
     if do_index:
         logger.info("Start generating index files to s3")
-        created_indexes = indexing.generate_indexes(top_level, valid_dirs, s3_client, bucket)
+        created_indexes = indexing.generate_indexes(
+            top_level, valid_dirs, s3_client, bucket, prefix_
+        )
         logger.info("Index files generation done.\n")
 
         logger.info("Start updating index files to s3")
         (_, _failed_metas) = s3_client.upload_metadatas(
             meta_file_paths=created_indexes,
             bucket_name=bucket,
-            product=None, root=top_level
+            product=None,
+            root=top_level,
+            key_prefix=prefix_
         )
         failed_metas.extend(_failed_metas)
         logger.info("Index files updating done\n")
@@ -275,6 +288,7 @@ def handle_maven_del(
     ignore_patterns=None,
     root="maven-repository",
     bucket_name=None,
+    prefix=None,
     dir_=None,
     do_index=True,
     dry_run=False
@@ -312,6 +326,7 @@ def handle_maven_del(
             logger.debug("G: %s, A: %s", g, a)
             ga_paths.append(os.path.join("/".join(g.split(".")), a))
 
+    prefix_ = remove_prefix(prefix, "/")
     # 4. Delete all valid_paths from s3
     logger.info("Start deleting files from s3")
     s3_client = S3Client(dry_run=dry_run)
@@ -320,13 +335,19 @@ def handle_maven_del(
         valid_mvn_paths,
         bucket_name=bucket,
         product=prod_key,
-        root=top_level
+        root=top_level,
+        key_prefix=prefix_
     )
     logger.info("Files deletion done\n")
 
     # 5. Use changed GA to scan s3 for metadata refreshment
     logger.info("Start generating maven-metadata.xml files for all changed GAs")
-    meta_files = _generate_metadatas(s3_client, bucket, valid_poms, top_level)
+    meta_files = _generate_metadatas(
+        s3=s3_client, bucket=bucket,
+        poms=valid_poms, root=top_level,
+        prefix=prefix_
+    )
+
     logger.info("maven-metadata.xml files generation done\n")
 
     # 6. Upload all maven-metadata.xml. We need to delete metadata files
@@ -336,7 +357,11 @@ def handle_maven_del(
     for _, files in meta_files.items():
         all_meta_files.extend(files)
     s3_client.delete_files(
-        file_paths=all_meta_files, bucket_name=bucket, product=prod_key, root=top_level
+        file_paths=all_meta_files,
+        bucket_name=bucket,
+        product=prod_key,
+        root=top_level,
+        key_prefix=prefix_
     )
     failed_metas = meta_files.get(META_FILE_FAILED, [])
     if META_FILE_GEN_KEY in meta_files:
@@ -344,14 +369,17 @@ def handle_maven_del(
             meta_file_paths=meta_files[META_FILE_GEN_KEY],
             bucket_name=bucket,
             product=None,
-            root=top_level
+            root=top_level,
+            key_prefix=prefix_
         )
         failed_metas.extend(_failed_metas)
     logger.info("maven-metadata.xml updating done\n")
 
     if do_index:
         logger.info("Start generating index files for all changed entries")
-        created_indexes = indexing.generate_indexes(top_level, valid_dirs, s3_client, bucket)
+        created_indexes = indexing.generate_indexes(
+            top_level, valid_dirs, s3_client, bucket, prefix_
+        )
         logger.info("Index files generation done.\n")
 
         logger.info("Start updating index to s3")
@@ -359,7 +387,8 @@ def handle_maven_del(
             meta_file_paths=created_indexes,
             bucket_name=bucket,
             product=None,
-            root=top_level
+            root=top_level,
+            key_prefix=prefix_
         )
         failed_metas.extend(_failed_index_files)
         logger.info("Index files updating done.\n")
@@ -445,7 +474,9 @@ def _scan_paths(files_root: str, ignore_patterns: List[str],
 
 
 def _generate_metadatas(
-    s3: S3Client, bucket: str, poms: List[str], root: str
+    s3: S3Client, bucket: str,
+    poms: List[str], root: str,
+    prefix: str = None
 ) -> Dict[str, List[str]]:
     """Collect GAVs and generating maven-metadata.xml.
        As all valid poms has been stored in s3 bucket,
@@ -467,9 +498,12 @@ def _generate_metadatas(
     for path, _ in gas_dict.items():
         # avoid some wrong prefix, like searching a/b
         # but got a/b-1
+        ga_prefix = path
+        if prefix:
+            ga_prefix = os.path.join(prefix, path)
         if not path.endswith("/"):
-            path = path + "/"
-        (existed_poms, success) = s3.get_files(bucket, path, ".pom")
+            ga_prefix = ga_prefix + "/"
+        (existed_poms, success) = s3.get_files(bucket, ga_prefix, ".pom")
         if len(existed_poms) == 0:
             if success:
                 logger.debug(
@@ -488,7 +522,13 @@ def _generate_metadatas(
             logger.debug(
                 "Got poms in s3 bucket %s for GA path %s: %s", bucket, path, poms
             )
-            all_poms.extend(existed_poms)
+            un_prefixed_poms = existed_poms
+            if prefix:
+                if not prefix.endswith("/"):
+                    un_prefixed_poms = [__remove_prefix(pom, prefix) for pom in existed_poms]
+                else:
+                    un_prefixed_poms = [__remove_prefix(pom, prefix + "/") for pom in existed_poms]
+            all_poms.extend(un_prefixed_poms)
     gav_dict = parse_gavs(all_poms)
     if len(gav_dict) > 0:
         meta_files_generation = []
@@ -524,6 +564,11 @@ def _handle_error(err_msgs: List[str]):
     pass
 
 
+def __remove_prefix(s: str, prefix: str) -> str:
+    if s.startswith(prefix):
+        return s[len(prefix):]
+
+
 class VersionCompareKey:
     'Used as key function for version sorting'
     def __init__(self, obj):
diff --git a/charon/pkgs/npm.py b/charon/pkgs/npm.py
index 8c69d5f4..8efca327 100644
--- a/charon/pkgs/npm.py
+++ b/charon/pkgs/npm.py
@@ -62,8 +62,9 @@ def __init__(self, metadata, is_version):
 
 def handle_npm_uploading(
         tarball_path: str, product: str,
-        bucket_name=None, dir_=None,
-        do_index=True, dry_run=False
+        bucket_name=None, prefix=None,
+        dir_=None, do_index=True,
+        dry_run=False
 ):
     """ Handle the npm product release tarball uploading process.
         For NPM uploading, tgz file and version metadata will be relocated based
@@ -76,7 +77,7 @@ def handle_npm_uploading(
           tmp dir if None.
     """
     target_dir, valid_paths, package_metadata = _scan_metadata_paths_from_archive(
-        tarball_path, prefix=product, dir__=dir_
+        tarball_path, prod=product, dir__=dir_
     )
     if not os.path.isdir(target_dir):
         logger.error("Error: the extracted target_dir path %s does not exist.", target_dir)
@@ -87,11 +88,12 @@ def handle_npm_uploading(
     logger.info("Start uploading files to s3")
     client = S3Client(dry_run=dry_run)
     bucket = bucket_name
-    uploaded_files = []
-    _uploaded_files, failed_files = client.upload_files(
-        file_paths=valid_paths, bucket_name=bucket, product=product, root=target_dir
+    _, failed_files = client.upload_files(
+        file_paths=valid_paths,
+        bucket_name=bucket,
+        product=product,
+        root=target_dir
     )
-    uploaded_files.extend(_uploaded_files)
     logger.info("Files uploading done\n")
 
     logger.info("Start generating package.json for package: %s", package_metadata.name)
@@ -102,28 +104,29 @@ def handle_npm_uploading(
 
     failed_metas = []
     if META_FILE_GEN_KEY in meta_files:
-        _uploaded_files, _failed_metas = client.upload_metadatas(
+        _, _failed_metas = client.upload_metadatas(
             meta_file_paths=[meta_files[META_FILE_GEN_KEY]],
             bucket_name=bucket,
             product=product,
             root=target_dir
         )
         failed_metas.extend(_failed_metas)
-        uploaded_files.extend(_uploaded_files)
         logger.info("package.json uploading done")
 
     # this step generates index.html for each dir and add them to file list
     # index is similar to metadata, it will be overwritten everytime
     if do_index:
         logger.info("Start generating index files to s3")
-        created_indexes = indexing.generate_indexes(target_dir, valid_dirs, client, bucket)
+        created_indexes = indexing.generate_indexes(
+            target_dir, valid_dirs, client, bucket, prefix
+        )
         logger.info("Index files generation done.\n")
 
         logger.info("Start updating index files to s3")
         (_, _failed_metas) = client.upload_metadatas(
             meta_file_paths=created_indexes,
-            bucket_name=bucket,
-            product=None, root=target_dir
+            bucket_name=bucket, product=None,
+            root=target_dir, key_prefix=prefix
         )
         failed_metas.extend(_failed_metas)
         logger.info("Index files updating done\n")
@@ -135,8 +138,9 @@ def handle_npm_uploading(
 
 def handle_npm_del(
         tarball_path: str, product: str,
-        bucket_name=None, dir_=None,
-        do_index=True, dry_run=False
+        bucket_name=None, prefix=None,
+        dir_=None, do_index=True,
+        dry_run=False
 ):
     """ Handle the npm product release tarball deletion process.
         * tarball_path is the location of the tarball in filesystem
@@ -147,7 +151,7 @@ def handle_npm_del(
           tmp dir if None.
     """
     target_dir, package_name_path, valid_paths = _scan_paths_from_archive(
-        tarball_path, prefix=product, dir__=dir_
+        tarball_path, prod=product, dir__=dir_
     )
 
     valid_dirs = __get_path_tree(valid_paths, target_dir)
@@ -156,12 +160,15 @@ def handle_npm_del(
     client = S3Client(dry_run=dry_run)
     bucket = bucket_name
     deleted_files, _ = client.delete_files(
-        file_paths=valid_paths, bucket_name=bucket, product=product, root=target_dir
+        file_paths=valid_paths, bucket_name=bucket,
+        product=product, root=target_dir
     )
     logger.info("Files deletion done\n")
 
     logger.info("Start generating package.json for package: %s", package_name_path)
-    meta_files = _gen_npm_package_metadata_for_del(client, bucket, target_dir, package_name_path)
+    meta_files = _gen_npm_package_metadata_for_del(
+        client, bucket, target_dir, package_name_path
+    )
     logger.info("package.json generation done\n")
 
     logger.info("Start uploading package.json to s3")
@@ -169,7 +176,8 @@ def handle_npm_del(
     for _, file in meta_files.items():
         all_meta_files.append(file)
     deleted_metas, failed_files = client.delete_files(
-        file_paths=all_meta_files, bucket_name=bucket, product=product, root=target_dir
+        file_paths=all_meta_files, bucket_name=bucket,
+        product=product, root=target_dir
     )
     deleted_files += deleted_metas
     failed_metas = []
@@ -190,7 +198,9 @@ def handle_npm_del(
 
     if do_index:
         logger.info("Start generating index files for all changed entries")
-        created_indexes = indexing.generate_indexes(target_dir, valid_dirs, client, bucket)
+        created_indexes = indexing.generate_indexes(
+            target_dir, valid_dirs, client, bucket, prefix
+        )
         logger.info("Index files generation done.\n")
 
         logger.info("Start updating index to s3")
@@ -198,7 +208,8 @@ def handle_npm_del(
             meta_file_paths=created_indexes,
             bucket_name=bucket,
             product=None,
-            root=target_dir
+            root=target_dir,
+            key_prefix=prefix
         )
         failed_metas.extend(_failed_index_files)
         logger.info("Index files updating done.\n")
@@ -289,9 +300,9 @@ def _gen_npm_package_metadata_for_del(
     return meta_files
 
 
-def _scan_metadata_paths_from_archive(path: str, prefix="", dir__=None) -> Tuple[
+def _scan_metadata_paths_from_archive(path: str, prod="", dir__=None) -> Tuple[
         str, list, NPMPackageMetadata]:
-    tmp_root = mkdtemp(prefix=f"npm-charon-{prefix}-", dir=dir__)
+    tmp_root = mkdtemp(prefix=f"npm-charon-{prod}-", dir=dir__)
     try:
         _, valid_paths = extract_npm_tarball(path, tmp_root, True)
         if len(valid_paths) > 1:
@@ -303,14 +314,15 @@ def _scan_metadata_paths_from_archive(path: str, prefix="", dir__=None) -> Tuple
         sys.exit(1)
 
 
-def _scan_paths_from_archive(path: str, prefix="", dir__=None) -> Tuple[str, str, list]:
-    tmp_root = mkdtemp(prefix=f"npm-charon-{prefix}-", dir=dir__)
+def _scan_paths_from_archive(path: str, prod="", dir__=None) -> Tuple[str, str, list]:
+    tmp_root = mkdtemp(prefix=f"npm-charon-{prod}-", dir=dir__)
     package_name_path, valid_paths = extract_npm_tarball(path, tmp_root, False)
     return tmp_root, package_name_path, valid_paths
 
 
 def _merge_package_metadata(
-        package_metadata: NPMPackageMetadata, client: S3Client, bucket: str,
+        package_metadata: NPMPackageMetadata,
+        client: S3Client, bucket: str,
         key: str
 ):
     content = client.read_file_content(bucket, key)
diff --git a/charon/storage.py b/charon/storage.py
index 26f91b2d..61b6ab40 100644
--- a/charon/storage.py
+++ b/charon/storage.py
@@ -86,7 +86,7 @@ def __enable_acceleration(self, extra_conf) -> bool:
 
     def upload_files(
         self, file_paths: List[str], bucket_name: str,
-        product: str, root="/"
+        product: str, root="/", key_prefix: str = None
     ) -> Tuple[List[str], List[str]]:
         """ Upload a list of files to s3 bucket. * Use the cut down file path as s3 key. The cut
         down way is move root from the file path if it starts with root. Example: if file_path is
@@ -115,7 +115,8 @@ def path_upload_handler(full_file_path: str, path: str) -> bool:
                                full_file_path, product)
                 return False
             logger.info('Uploading %s to bucket %s', full_file_path, bucket_name)
-            fileObject = bucket.Object(path)
+            path_key = os.path.join(key_prefix, path) if key_prefix else path
+            fileObject = bucket.Object(path_key)
             existed = self.file_exists(fileObject)
             sha1 = read_sha1(full_file_path)
             (content_type, _) = mimetypes.guess_type(full_file_path)
@@ -141,7 +142,7 @@ def path_upload_handler(full_file_path: str, path: str) -> bool:
                                 ExtraArgs={'ContentType': content_type}
                             )
                     logger.info('Uploaded %s to bucket %s', full_file_path, bucket_name)
-                    uploaded_files.append(path)
+                    uploaded_files.append(path_key)
                 except (ClientError, HTTPClientError) as e:
                     logger.error("ERROR: file %s not uploaded to bucket"
                                  " %s due to error: %s ", full_file_path,
@@ -158,7 +159,7 @@ def path_upload_handler(full_file_path: str, path: str) -> bool:
                 )
                 if checksum != "" and checksum.strip() != sha1:
                     logger.error('Error: checksum check failed. The file %s is different from the '
-                                 'one in S3. Product: %s', path, product)
+                                 'one in S3. Product: %s', path_key, product)
                     return False
 
                 prods = []
@@ -173,7 +174,7 @@ def path_upload_handler(full_file_path: str, path: str) -> bool:
                         product,
                     )
                     prods.append(product)
-                    self.__update_file_metadata(fileObject, bucket_name, path,
+                    self.__update_file_metadata(fileObject, bucket_name, path_key,
                                                 {PRODUCT_META_KEY: ",".join(prods)})
             return True
 
@@ -183,7 +184,7 @@ def path_upload_handler(full_file_path: str, path: str) -> bool:
 
     def upload_metadatas(
         self, meta_file_paths: List[str], bucket_name: str,
-        product: str, root="/"
+        product: str, root="/", key_prefix: str = None
     ) -> Tuple[List[str], List[str]]:
         """ Upload a list of metadata files to s3 bucket. This function is very similar to
         upload_files, except:
@@ -201,7 +202,8 @@ def path_upload_handler(full_file_path: str, path: str):
                                full_file_path, product)
                 return False
             logger.info('Updating metadata %s to bucket %s', path, bucket_name)
-            fileObject = bucket.Object(path)
+            path_key = os.path.join(key_prefix, path) if key_prefix else path
+            fileObject = bucket.Object(path_key)
             existed = self.file_exists(fileObject)
             f_meta = {}
             need_overwritten = True
@@ -233,9 +235,9 @@ def path_upload_handler(full_file_path: str, path: str):
                             ContentType=content_type
                         )
                     else:
-                        self.__update_file_metadata(fileObject, bucket_name, path, f_meta)
+                        self.__update_file_metadata(fileObject, bucket_name, path_key, f_meta)
                 logger.info('Updated metadata %s to bucket %s', path, bucket_name)
-                uploaded_files.append(path)
+                uploaded_files.append(path_key)
             except (ClientError, HTTPClientError) as e:
                 logger.error("ERROR: file %s not uploaded to bucket"
                              " %s due to error: %s ", full_file_path,
@@ -248,7 +250,8 @@ def path_upload_handler(full_file_path: str, path: str):
         ))
 
     def delete_files(
-        self, file_paths: List[str], bucket_name: str, product: str, root="/"
+        self, file_paths: List[str], bucket_name: str,
+        product: str, root="/", key_prefix: str = None
     ) -> Tuple[List[str], List[str]]:
         """ Deletes a list of files to s3 bucket. * Use the cut down file path as s3 key. The cut
         down way is move root from the file path if it starts with root. Example: if file_path is
@@ -266,7 +269,8 @@ def delete_files(
 
         def path_delete_handler(full_file_path: str, path: str):
             logger.info('Deleting %s from bucket %s', path, bucket_name)
-            fileObject = bucket.Object(path)
+            path_key = os.path.join(key_prefix, path) if key_prefix else path
+            fileObject = bucket.Object(path_key)
             existed = self.file_exists(fileObject)
             if existed:
                 prods = []
@@ -286,7 +290,7 @@ def path_delete_handler(full_file_path: str, path: str):
                         self.__update_file_metadata(
                             fileObject,
                             bucket_name,
-                            path,
+                            path_key,
                             {PRODUCT_META_KEY: ",".join(prods)},
                         )
                         logger.info(
@@ -303,7 +307,7 @@ def path_delete_handler(full_file_path: str, path: str):
                 elif len(prods) == 0:
                     try:
                         if not self.dry_run:
-                            bucket.delete_objects(Delete={"Objects": [{"Key": path}]})
+                            bucket.delete_objects(Delete={"Objects": [{"Key": path_key}]})
                         logger.info("Deleted %s from bucket %s", path, bucket_name)
                         deleted_files.append(path)
                         return True
@@ -416,7 +420,8 @@ def __update_file_metadata(
             )
 
     def __do_path_cut_and(
-        self, file_paths: List[str], fn: Callable[[str, str], bool], root="/"
+        self, file_paths: List[str],
+        fn: Callable[[str, str], bool], root="/"
     ) -> List[str]:
         slash_root = root
         if not root.endswith("/"):
diff --git a/charon/utils/archive.py b/charon/utils/archive.py
index 3dba1ec5..9b46858c 100644
--- a/charon/utils/archive.py
+++ b/charon/utils/archive.py
@@ -149,7 +149,7 @@ def download_archive(url: str, base_dir=None) -> str:
     local_filename = os.path.join(dir_, url.split('/')[-1])
     # NOTE the stream=True parameter below
     # NOTE(2) timeout=30 parameter to set a 30-second timeout, and prevent indefinite hang.
-    with requests.get(url, stream=True, timeout=30) as r:
+    with requests.get(url, stream=True, timeout=30, verify=False) as r:
         r.raise_for_status()
         with open(local_filename, 'wb') as f:
             for chunk in r.iter_content(chunk_size=8192):
diff --git a/charon/utils/strings.py b/charon/utils/strings.py
new file mode 100644
index 00000000..a3f0ff59
--- /dev/null
+++ b/charon/utils/strings.py
@@ -0,0 +1,4 @@
+def remove_prefix(string: str, prefix: str) -> str:
+    if string and prefix and string.startswith(prefix):
+        return string[len(prefix):]
+    return string
diff --git a/tests/base.py b/tests/base.py
index 37ac4e76..1eaee35e 100644
--- a/tests/base.py
+++ b/tests/base.py
@@ -20,6 +20,9 @@
 from charon.utils.files import write_file
 from charon.config import CONFIG_FILE
 
+SHORT_TEST_PREFIX = "ga"
+LONG_TEST_PREFIX = "earlyaccess/all"
+
 
 class BaseTest(unittest.TestCase):
     def setUp(self):
diff --git a/tests/test_maven_del.py b/tests/test_maven_del.py
index d5fcbc0c..f079dbe5 100644
--- a/tests/test_maven_del.py
+++ b/tests/test_maven_del.py
@@ -1,6 +1,7 @@
 from charon.pkgs.maven import handle_maven_uploading, handle_maven_del
 from charon.storage import PRODUCT_META_KEY, CHECKSUM_META_KEY
-from tests.base import BaseTest
+from charon.utils.strings import remove_prefix
+from tests.base import LONG_TEST_PREFIX, SHORT_TEST_PREFIX, BaseTest
 from moto import mock_s3
 import boto3
 import os
@@ -184,17 +185,87 @@ def test_ignore_del(self):
         for f in non_sha1_files:
             self.assertNotIn(f, actual_files)
 
-    def __prepare_content(self):
+    def test_short_prefix_deletion(self):
+        self.__test_prefix_deletion(SHORT_TEST_PREFIX)
+
+    def test_long_prefix_deletion(self):
+        self.__test_prefix_deletion(LONG_TEST_PREFIX)
+
+    def test_root_prefix_deletion(self):
+        self.__test_prefix_deletion("/")
+
+    def __test_prefix_deletion(self, prefix: str):
+        self.__prepare_content(prefix)
+
+        test_zip = os.path.join(os.getcwd(), "tests/input/commons-client-4.5.6.zip")
+        product_456 = "commons-client-4.5.6"
+        handle_maven_del(
+            test_zip, product_456,
+            bucket_name=TEST_BUCKET,
+            prefix=prefix,
+            dir_=self.tempdir, do_index=False
+        )
+
+        test_bucket = self.mock_s3.Bucket(TEST_BUCKET)
+        objs = list(test_bucket.objects.all())
+        actual_files = [obj.key for obj in objs]
+        self.assertEqual(12, len(actual_files))
+
+        prefix_ = remove_prefix(prefix, "/")
+        PREFIXED_COMMONS_CLIENT_456_FILES = [
+            os.path.join(prefix_, f) for f in COMMONS_CLIENT_456_FILES]
+        for f in PREFIXED_COMMONS_CLIENT_456_FILES:
+            self.assertNotIn(f, actual_files)
+        PREFIXED_COMMONS_CLIENT_META = os.path.join(prefix_, COMMONS_CLIENT_META)
+        self.assertIn(PREFIXED_COMMONS_CLIENT_META, actual_files)
+
+        PREFIXED_COMMONS_LOGGING_FILES = [
+            os.path.join(prefix_, f) for f in COMMONS_LOGGING_FILES]
+        for f in PREFIXED_COMMONS_LOGGING_FILES:
+            self.assertIn(f, actual_files)
+        PREFIXED_COMMONS_LOGGING_META = os.path.join(prefix_, COMMONS_LOGGING_META)
+        self.assertIn(PREFIXED_COMMONS_LOGGING_META, actual_files)
+
+        for obj in objs:
+            self.assertIn(CHECKSUM_META_KEY, obj.Object().metadata)
+            self.assertNotEqual("", obj.Object().metadata[CHECKSUM_META_KEY].strip())
+
+        product_459 = "commons-client-4.5.9"
+        meta_obj_client = test_bucket.Object(PREFIXED_COMMONS_CLIENT_META)
+        self.assertEqual(product_459, meta_obj_client.metadata[PRODUCT_META_KEY])
+
+        meta_obj_logging = test_bucket.Object(PREFIXED_COMMONS_LOGGING_META)
+        self.assertEqual(product_459, meta_obj_logging.metadata[PRODUCT_META_KEY])
+
+        test_zip = os.path.join(os.getcwd(), "tests/input/commons-client-4.5.9.zip")
+        handle_maven_del(
+            test_zip, product_459,
+            bucket_name=TEST_BUCKET,
+            prefix=prefix,
+            dir_=self.tempdir,
+            do_index=False
+        )
+
+        objs = list(test_bucket.objects.all())
+        self.assertEqual(0, len(objs))
+
+    def __prepare_content(self, prefix=None):
         test_zip = os.path.join(os.getcwd(), "tests/input/commons-client-4.5.6.zip")
         product_456 = "commons-client-4.5.6"
         handle_maven_uploading(
             test_zip, product_456,
-            bucket_name=TEST_BUCKET, dir_=self.tempdir, do_index=False
+            bucket_name=TEST_BUCKET,
+            prefix=prefix,
+            dir_=self.tempdir,
+            do_index=False
         )
 
         test_zip = os.path.join(os.getcwd(), "tests/input/commons-client-4.5.9.zip")
         product_459 = "commons-client-4.5.9"
         handle_maven_uploading(
             test_zip, product_459,
-            bucket_name=TEST_BUCKET, dir_=self.tempdir, do_index=False
+            bucket_name=TEST_BUCKET,
+            prefix=prefix,
+            dir_=self.tempdir,
+            do_index=False
         )
diff --git a/tests/test_maven_index.py b/tests/test_maven_index.py
index 8e021a79..1fb0b4d5 100644
--- a/tests/test_maven_index.py
+++ b/tests/test_maven_index.py
@@ -15,7 +15,8 @@
 """
 from charon.pkgs.maven import handle_maven_uploading, handle_maven_del
 from charon.storage import CHECKSUM_META_KEY
-from tests.base import BaseTest
+from charon.utils.strings import remove_prefix
+from tests.base import LONG_TEST_PREFIX, SHORT_TEST_PREFIX, BaseTest
 from moto import mock_s3
 import boto3
 import os
@@ -162,6 +163,66 @@ def test_overlap_upload_index(self):
         )
         self.assertNotIn("<a href=\"../index.html\" title=\"../\">../</a>", index_content)
 
+    def test_upload_index_with_short_prefix(self):
+        self.__test_upload_index_with_prefix(SHORT_TEST_PREFIX)
+
+    def test_upload_index_with_long_prefix(self):
+        self.__test_upload_index_with_prefix(LONG_TEST_PREFIX)
+
+    def test_upload_index_with_root_prefix(self):
+        self.__test_upload_index_with_prefix("/")
+
+    def __test_upload_index_with_prefix(self, prefix: str):
+        test_zip = os.path.join(os.getcwd(), "tests/input/commons-client-4.5.6.zip")
+        product = "commons-client-4.5.6"
+        handle_maven_uploading(
+            test_zip, product,
+            bucket_name=TEST_BUCKET,
+            dir_=self.tempdir,
+            prefix=prefix
+        )
+
+        test_bucket = self.mock_s3.Bucket(TEST_BUCKET)
+        objs = list(test_bucket.objects.all())
+        actual_files = [obj.key for obj in objs]
+        self.assertEqual(21, len(actual_files))
+
+        prefix_ = remove_prefix(prefix, "/")
+        PREFIXED_LOGGING_INDEXES = [
+            os.path.join(prefix_, i) for i in COMMONS_LOGGING_INDEXES
+        ]
+        for f in PREFIXED_LOGGING_INDEXES:
+            self.assertIn(f, actual_files)
+
+        PREFIXED_456_INDEXES = [
+            os.path.join(prefix_, i) for i in COMMONS_CLIENT_456_INDEXES
+        ]
+        for f in PREFIXED_456_INDEXES:
+            self.assertIn(f, actual_files)
+
+        for obj in objs:
+            self.assertIn(CHECKSUM_META_KEY, obj.Object().metadata)
+            self.assertNotEqual("", obj.Object().metadata[CHECKSUM_META_KEY].strip())
+
+        indedx_obj = test_bucket.Object(os.path.join(prefix_, COMMONS_CLIENT_INDEX))
+        index_content = str(indedx_obj.get()["Body"].read(), "utf-8")
+        self.assertIn("<a href=\"4.5.6/index.html\" title=\"4.5.6/\">4.5.6/</a>", index_content)
+        self.assertIn(
+            "<a href=\"maven-metadata.xml\" title=\"maven-metadata.xml\">maven-metadata.xml</a>",
+            index_content
+        )
+        self.assertIn("<a href=\"../index.html\" title=\"../\">../</a>", index_content)
+
+        indedx_obj = test_bucket.Object(os.path.join(prefix_, COMMONS_ROOT_INDEX))
+        index_content = str(indedx_obj.get()["Body"].read(), "utf-8")
+        self.assertIn("<a href=\"org/index.html\" title=\"org/\">org/</a>", index_content)
+        self.assertIn(
+            "<a href=\"commons-logging/index.html\" "
+            "title=\"commons-logging/\">commons-logging/</a>",
+            index_content
+        )
+        self.assertNotIn("<a href=\"../index.html\" title=\"../\">../</a>", index_content)
+
     def test_deletion_index(self):
         self.__prepare_content()
 
@@ -218,12 +279,85 @@ def test_deletion_index(self):
         objs = list(test_bucket.objects.all())
         self.assertEqual(0, len(objs))
 
-    def __prepare_content(self):
+    def test_deletion_index_with_short_prefix(self):
+        self.__test_deletion_index_with_prefix(SHORT_TEST_PREFIX)
+
+    def test_deletion_index_with_long_prefix(self):
+        self.__test_deletion_index_with_prefix(LONG_TEST_PREFIX)
+
+    def test_deletion_index_with_root_prefix(self):
+        self.__test_deletion_index_with_prefix("/")
+
+    def __test_deletion_index_with_prefix(self, prefix: str):
+        self.__prepare_content(prefix)
+
+        test_zip = os.path.join(os.getcwd(), "tests/input/commons-client-4.5.6.zip")
+        product_456 = "commons-client-4.5.6"
+        handle_maven_del(
+            test_zip, product_456,
+            bucket_name=TEST_BUCKET,
+            prefix=prefix,
+            dir_=self.tempdir
+        )
+
+        test_bucket = self.mock_s3.Bucket(TEST_BUCKET)
+        objs = list(test_bucket.objects.all())
+        actual_files = [obj.key for obj in objs]
+        self.assertEqual(21, len(actual_files))
+
+        prefix_ = remove_prefix(prefix, "/")
+        PREFIXED_459_INDEXES = [os.path.join(prefix_, i) for i in COMMONS_CLIENT_459_INDEXES]
+        for assert_file in PREFIXED_459_INDEXES:
+            self.assertIn(assert_file, actual_files)
+
+        PREFIXED_LOGGING_INDEXES = [os.path.join(prefix_, i) for i in COMMONS_LOGGING_INDEXES]
+        for assert_file in PREFIXED_LOGGING_INDEXES:
+            self.assertIn(assert_file, actual_files)
+
+        self.assertNotIn(os.path.join(prefix_, COMMONS_CLIENT_456_INDEX), actual_files)
+
+        for obj in objs:
+            self.assertIn(CHECKSUM_META_KEY, obj.Object().metadata)
+            self.assertNotEqual("", obj.Object().metadata[CHECKSUM_META_KEY].strip())
+
+        indedx_obj = test_bucket.Object(os.path.join(prefix_, COMMONS_CLIENT_INDEX))
+        index_content = str(indedx_obj.get()["Body"].read(), "utf-8")
+        self.assertIn("<a href=\"4.5.9/index.html\" title=\"4.5.9/\">4.5.9/</a>", index_content)
+        self.assertIn("<a href=\"../index.html\" title=\"../\">../</a>", index_content)
+        self.assertIn(
+            "<a href=\"maven-metadata.xml\" title=\"maven-metadata.xml\">maven-metadata.xml</a>",
+            index_content)
+        self.assertNotIn("<a href=\"4.5.6/index.html\" title=\"4.5.6/\">4.5.6/</a>", index_content)
+
+        indedx_obj = test_bucket.Object(os.path.join(prefix_, COMMONS_ROOT_INDEX))
+        index_content = str(indedx_obj.get()["Body"].read(), "utf-8")
+        self.assertIn("<a href=\"org/index.html\" title=\"org/\">org/</a>", index_content)
+        self.assertIn(
+            "<a href=\"commons-logging/index.html\" "
+            "title=\"commons-logging/\">commons-logging/</a>",
+            index_content
+        )
+        self.assertNotIn("<a href=\"../index.html\" title=\"../\">../</a>", index_content)
+
+        product_459 = "commons-client-4.5.9"
+        test_zip = os.path.join(os.getcwd(), "tests/input/commons-client-4.5.9.zip")
+        handle_maven_del(
+            test_zip, product_459,
+            bucket_name=TEST_BUCKET,
+            prefix=prefix,
+            dir_=self.tempdir
+        )
+
+        objs = list(test_bucket.objects.all())
+        self.assertEqual(0, len(objs))
+
+    def __prepare_content(self, prefix=None):
         test_zip = os.path.join(os.getcwd(), "tests/input/commons-client-4.5.6.zip")
         product_456 = "commons-client-4.5.6"
         handle_maven_uploading(
             test_zip, product_456,
             bucket_name=TEST_BUCKET,
+            prefix=prefix,
             dir_=self.tempdir
         )
 
@@ -232,5 +366,6 @@ def __prepare_content(self):
         handle_maven_uploading(
             test_zip, product_459,
             bucket_name=TEST_BUCKET,
+            prefix=prefix,
             dir_=self.tempdir
         )
diff --git a/tests/test_maven_upload.py b/tests/test_maven_upload.py
index f5a1ced6..45d1351f 100644
--- a/tests/test_maven_upload.py
+++ b/tests/test_maven_upload.py
@@ -1,6 +1,7 @@
 from charon.pkgs.maven import handle_maven_uploading
 from charon.storage import PRODUCT_META_KEY, CHECKSUM_META_KEY
-from tests.base import BaseTest
+from charon.utils.strings import remove_prefix
+from tests.base import BaseTest, SHORT_TEST_PREFIX, LONG_TEST_PREFIX
 from moto import mock_s3
 import boto3
 import os
@@ -215,3 +216,59 @@ def test_ignore_upload(self):
 
         for f in ignored_files:
             self.assertNotIn(f, actual_files)
+
+    def test_short_prefix_upload(self):
+        self.__test_prefix_upload(SHORT_TEST_PREFIX)
+
+    def test_long_prefix_upload(self):
+        self.__test_prefix_upload(LONG_TEST_PREFIX)
+
+    def test_root_prefix_upload(self):
+        self.__test_prefix_upload("/")
+
+    def __test_prefix_upload(self, prefix: str):
+        test_zip = os.path.join(os.getcwd(), "tests/input/commons-client-4.5.6.zip")
+        product = "commons-client-4.5.6"
+        handle_maven_uploading(
+            test_zip, product,
+            bucket_name=TEST_BUCKET,
+            prefix=prefix,
+            dir_=self.tempdir,
+            do_index=False
+        )
+
+        test_bucket = self.mock_s3.Bucket(TEST_BUCKET)
+        objs = list(test_bucket.objects.all())
+        actual_files = [obj.key for obj in objs]
+        self.assertEqual(12, len(actual_files))
+
+        prefix_ = remove_prefix(prefix, "/")
+        PREFIXED_COMMONS_CLIENT_456_FILES = [
+            os.path.join(prefix_, f) for f in COMMONS_CLIENT_456_FILES]
+        for f in PREFIXED_COMMONS_CLIENT_456_FILES:
+            self.assertIn(f, actual_files)
+        PREFIXED_COMMONS_CLIENT_META = os.path.join(prefix_, COMMONS_CLIENT_META)
+        self.assertIn(PREFIXED_COMMONS_CLIENT_META, actual_files)
+
+        PREFIXED_COMMONS_LOGGING_FILES = [
+            os.path.join(prefix_, f) for f in COMMONS_LOGGING_FILES]
+        for f in PREFIXED_COMMONS_LOGGING_FILES:
+            self.assertIn(f, actual_files)
+        PREFIXED_COMMONS_LOGGING_META = os.path.join(prefix_, COMMONS_LOGGING_META)
+        self.assertIn(PREFIXED_COMMONS_LOGGING_META, actual_files)
+
+        PREFIXED_NON_MVN_FILES = [
+            os.path.join(prefix_, f) for f in NON_MVN_FILES]
+        for f in PREFIXED_NON_MVN_FILES:
+            self.assertNotIn(f, actual_files)
+
+        for obj in objs:
+            self.assertEqual(product, obj.Object().metadata[PRODUCT_META_KEY])
+            self.assertIn(CHECKSUM_META_KEY, obj.Object().metadata)
+            self.assertNotEqual("", obj.Object().metadata[CHECKSUM_META_KEY].strip())
+
+        meta_obj_client = test_bucket.Object(PREFIXED_COMMONS_CLIENT_META)
+        self.assertIsNotNone(meta_obj_client)
+
+        meta_obj_logging = test_bucket.Object(PREFIXED_COMMONS_LOGGING_META)
+        self.assertIsNotNone(meta_obj_logging)
diff --git a/tests/test_s3client.py b/tests/test_s3client.py
index 6dc7aeb7..596c14db 100644
--- a/tests/test_s3client.py
+++ b/tests/test_s3client.py
@@ -16,7 +16,7 @@
 from charon.storage import S3Client, PRODUCT_META_KEY, CHECKSUM_META_KEY
 from charon.utils.archive import extract_zip_all
 from charon.utils.files import write_file, read_sha1
-from tests.base import BaseTest
+from tests.base import BaseTest, SHORT_TEST_PREFIX
 from moto import mock_s3
 import boto3
 import os
@@ -185,6 +185,34 @@ def test_upload_and_delete_files(self):
 
         shutil.rmtree(temp_root)
 
+    def test_upload_and_delete_with_prefix(self):
+        (temp_root, root, all_files) = self.__prepare_files()
+        test_files = list(filter(lambda f: f.startswith(root), all_files))
+
+        bucket = self.mock_s3.Bucket(MY_BUCKET)
+
+        self.s3_client.upload_files(
+            test_files,
+            bucket_name=MY_BUCKET,
+            product="apache-commons",
+            root=root,
+            key_prefix=SHORT_TEST_PREFIX)
+        objects = list(bucket.objects.all())
+        self.assertEqual(COMMONS_LANG3_ZIP_ENTRY - 4, len(objects))
+        for obj in objects:
+            self.assertTrue(obj.key.startswith(SHORT_TEST_PREFIX))
+
+        self.s3_client.delete_files(
+            file_paths=test_files,
+            bucket_name=MY_BUCKET,
+            product="apache-commons",
+            root=root,
+            key_prefix=SHORT_TEST_PREFIX)
+        objects = list(bucket.objects.all())
+        self.assertEqual(0, len(list(bucket.objects.all())))
+
+        shutil.rmtree(temp_root)
+
     def test_upload_file_with_checksum(self):
         temp_root = os.path.join(self.tempdir, "tmp_upd")
         os.mkdir(temp_root)