diff --git a/conan/api/subapi/cache.py b/conan/api/subapi/cache.py
index 36068942d28..8c8db46a87e 100644
--- a/conan/api/subapi/cache.py
+++ b/conan/api/subapi/cache.py
@@ -181,13 +181,19 @@ def restore(self, path):
                 pkg_folder = pref_bundle["package_folder"]
                 out.info(f"Restore: {pref} in {pkg_folder}")
                 # We need to put the package in the final location in the cache
+                if os.path.exists(pkg_layout.package()) and pkg_layout.package() != os.path.join(cache.cache_folder, pkg_folder):
+                    shutil.rmtree(pkg_layout.package())
                 shutil.move(os.path.join(cache.cache_folder, pkg_folder), pkg_layout.package())
+                pref_bundle["package_folder"] = os.path.relpath(pkg_layout.package(), cache.cache_folder)
                 metadata_folder = pref_bundle.get("metadata_folder")
                 if metadata_folder:
                     out.info(f"Restore: {pref} metadata in {metadata_folder}")
                     # We need to put the package in the final location in the cache
+                    if os.path.exists(pkg_layout.metadata()) and pkg_layout.metadata() != os.path.join(cache.cache_folder, metadata_folder):
+                        shutil.rmtree(pkg_layout.metadata())
                     shutil.move(os.path.join(cache.cache_folder, metadata_folder),
                                 pkg_layout.metadata())
+                    pref_bundle["metadata_folder"] = os.path.relpath(pkg_layout.metadata(), cache.cache_folder)
 
         return package_list
 
diff --git a/conans/test/integration/command_v2/test_cache_save_restore.py b/conans/test/integration/command_v2/test_cache_save_restore.py
index e178cf240b2..046e0fb0e96 100644
--- a/conans/test/integration/command_v2/test_cache_save_restore.py
+++ b/conans/test/integration/command_v2/test_cache_save_restore.py
@@ -30,6 +30,36 @@ def test_cache_save_restore():
     assert "\\" not in package_list
 
 
+def test_cache_save_restore_with_package_file():
+    """If we have some sources in the root (like the CMakeLists.txt)
+    we don't declare folders.source"""
+    conan_file = GenConanfile() \
+        .with_settings("os") \
+        .with_package_file("bin/file.txt", "content!!")
+
+    client = TestClient()
+    client.save({"conanfile.py": conan_file})
+    client.run("create . --name=pkg --version=1.0 -s os=Linux")
+    client.run("cache save pkg/*:* ")
+    cache_path = os.path.join(client.current_folder, "conan_cache_save.tgz")
+    assert os.path.exists(cache_path)
+
+    c2 = TestClient()
+    shutil.copy2(cache_path, c2.current_folder)
+    c2.run("cache restore conan_cache_save.tgz")
+    c2.run("list *:*#*")
+    assert "pkg/1.0" in c2.out
+    tree = _get_directory_tree(c2.base_folder)
+
+    # Restore again, expect the tree to be unchanged
+    c2.run("cache restore conan_cache_save.tgz")
+    c2.run("list *:*#*")
+    assert "pkg/1.0" in c2.out
+    tree2 = _get_directory_tree(c2.base_folder)
+
+    assert tree2 == tree
+
+
 def test_cache_save_downloaded_restore():
     """ what happens if we save packages downloaded from server, not
     created
@@ -49,6 +79,18 @@ def test_cache_save_downloaded_restore():
     _validate_restore(cache_path)
 
 
+def _get_directory_tree(base_folder):
+    tree = []
+    for d, _, fs in os.walk(base_folder):
+        rel_d = os.path.relpath(d, base_folder) if d != base_folder else ""
+        if rel_d:
+            tree.append(rel_d)
+        for f in fs:
+            tree.append(os.path.join(rel_d, f))
+    tree.sort()
+    return tree
+
+
 def _validate_restore(cache_path):
     c2 = TestClient()
     # Create a package in the cache to check put doesn't interact badly
@@ -61,6 +103,7 @@ def _validate_restore(cache_path):
     assert "pkg/1.0" in c2.out
     assert "pkg/1.1" in c2.out
     assert "other/2.0" not in c2.out
+    tree = _get_directory_tree(c2.base_folder)
 
     # Restore again, just in case
     c2.run("cache restore conan_cache_save.tgz")
@@ -69,6 +112,8 @@ def _validate_restore(cache_path):
     assert "pkg/1.0" in c2.out
     assert "pkg/1.1" in c2.out
     assert "other/2.0" not in c2.out
+    tree2 = _get_directory_tree(c2.base_folder)
+    assert tree2 == tree
 
 
 def test_cache_save_restore_metadata():