diff --git a/lib/configuration/command_configuration.ml b/lib/configuration/command_configuration.ml
index 163d332d..39e080b8 100644
--- a/lib/configuration/command_configuration.ml
+++ b/lib/configuration/command_configuration.ml
@@ -54,7 +54,8 @@ let parse_source_directories ?(file_filters = []) exclude_directory_prefix targe
             Continue acc
         else
           begin
-            if String.is_prefix (Filename.basename absolute_path) ~prefix:exclude_directory_prefix then
+            if List.exists exclude_directory_prefix
+                ~f:(fun prefix -> String.is_prefix (Filename.basename absolute_path) ~prefix) then
               Skip acc
             else
               Continue acc
@@ -142,7 +143,7 @@ type user_input_options =
   ; match_only : bool
   ; target_directory : string
   ; directory_depth : int option
-  ; exclude_directory_prefix : string
+  ; exclude_directory_prefix : string list
   }
 
 type run_options =
@@ -337,7 +338,7 @@ type t =
   { sources : Command_input.t
   ; specifications : Specification.t list
   ; file_filters : string list option
-  ; exclude_directory_prefix : string
+  ; exclude_directory_prefix : string list
   ; run_options : run_options
   ; output_printer : Printer.t
   ; interactive_review : interactive_review option
@@ -526,7 +527,7 @@ let create
   let sources =
     match input_source with
     | Stdin -> `String (In_channel.input_all In_channel.stdin)
-    (* TODO(RVT): Unify exclude-dir handling. Currently exclude-dir option must be done while processing zip file in main.ml. *)
+    (* TODO(RVT): Unify exclude-dir handling. Currently the exclude-dir option for zip file is done in pipeline.ml and not here. *)
     | Zip -> `Zip (Option.value_exn zip_file)
     | Directory ->
       let target_directory =
diff --git a/lib/configuration/command_configuration.mli b/lib/configuration/command_configuration.mli
index 66e80029..df15ea5d 100644
--- a/lib/configuration/command_configuration.mli
+++ b/lib/configuration/command_configuration.mli
@@ -49,7 +49,7 @@ type user_input_options =
   ; match_only : bool
   ; target_directory : string
   ; directory_depth : int option
-  ; exclude_directory_prefix : string
+  ; exclude_directory_prefix : string list
   }
 
 type run_options =
@@ -72,7 +72,7 @@ type t =
   { sources : Command_input.t
   ; specifications : Specification.t list
   ; file_filters : string list option
-  ; exclude_directory_prefix : string
+  ; exclude_directory_prefix : string list
   ; run_options : run_options
   ; output_printer : Printer.t
   ; interactive_review : interactive_review option
diff --git a/lib/pipeline/pipeline.ml b/lib/pipeline/pipeline.ml
index c75c03e6..350ee8ed 100644
--- a/lib/pipeline/pipeline.ml
+++ b/lib/pipeline/pipeline.ml
@@ -299,17 +299,19 @@ let process_paths_for_interactive ~sequential ~f paths scheduler =
     with_scheduler scheduler ~f:(try_or_skip f ~default:([],0))
 
 let filter_zip_entries file_filters exclude_directory_prefix zip =
-  let not_in_an_exclude_directory prefix filename = not (String.is_prefix ~prefix filename) in
+  let exclude_the_directory prefixes filename =
+    List.exists prefixes ~f:(fun prefix -> String.is_prefix ~prefix filename)
+  in
   match file_filters with
   | Some [] | None -> List.filter (Zip.entries zip) ~f:(fun { is_directory; filename; _ } ->
-      not is_directory && not_in_an_exclude_directory exclude_directory_prefix filename)
+      not is_directory && not (exclude_the_directory exclude_directory_prefix filename))
   | Some suffixes ->
     let has_acceptable_suffix filename =
       List.exists suffixes ~f:(fun suffix -> String.is_suffix ~suffix filename)
     in
     List.filter (Zip.entries zip) ~f:(fun { is_directory; filename; _ } ->
         not is_directory
-        && not_in_an_exclude_directory exclude_directory_prefix filename
+        && not (exclude_the_directory exclude_directory_prefix filename)
         && has_acceptable_suffix filename)
 
 let process_zip_file ~sequential ~f scheduler zip_file exclude_directory_prefix file_filters =
diff --git a/src/main.ml b/src/main.ml
index a570271e..fd2fc902 100644
--- a/src/main.ml
+++ b/src/main.ml
@@ -128,7 +128,7 @@ let base_command_parameters : (unit -> 'result) Command.Param.t =
     and newline_separated_rewrites = flag "newline-separated" no_arg ~doc:"Instead of rewriting in place, output rewrites separated by newlines."
     and count = flag "count" no_arg ~doc:"Display a count of matches in a file."
     and list = flag "list" no_arg ~doc:"Display supported languages and extensions"
-    and exclude_directory_prefix = flag "exclude-dir" (optional_with_default "." string) ~doc:"prefix of directories to exclude. Default: '.'"
+    and exclude_directory_prefix = flag "exclude-dir" (optional_with_default ["."] (Arg_type.comma_separated ~strip_whitespace:true string)) ~doc:"prefixes Comma-separated prefixes of directories to exclude. Do not put whitespace between commas unless the string is quoted. Default: '.' (ignore directories starting with dot)"
     and interactive_review = flag "review" ~aliases:["r"] no_arg ~doc:"Review each patch and accept, reject, or modify it with your editor of choice. Defaults to $EDITOR. If $EDITOR is unset, defaults to \"vim\". Override $EDITOR with the -editor flag."
     and editor = flag "editor" (optional string) ~doc:"editor Perform manual review with [editor]. This activates -review mode."
     and editor_default_is_reject = flag "default-no" no_arg ~doc:"If set, the default action in review (pressing return) will NOT apply the change. Setting this option activates -review mode."
diff --git a/test/common/test_cli.ml b/test/common/test_cli.ml
index 4081ec61..2384eb91 100644
--- a/test/common/test_cli.ml
+++ b/test/common/test_cli.ml
@@ -480,7 +480,8 @@ let%expect_test "is_real_directory" =
 let%expect_test "exclude_dir_option" =
   let source = "hello world" in
   let src_dir = "example" ^/ "src" in
-  let command_args = Format.sprintf "'main' 'pain' -sequential -d %s -exclude-dir 'ignore' -diff" src_dir in
+  let exclude_dir = "ignore,also-ignore" in
+  let command_args = Format.sprintf "'main' 'pain' -sequential -d %s -exclude-dir %s -diff" src_dir exclude_dir in
   let command = Format.sprintf "%s %s" binary_path command_args in
   let result = read_expect_stdin_and_stdout command source in
   print_string result;
@@ -514,6 +515,11 @@ let%expect_test "exclude_dir_option" =
   let result = read_expect_stdin_and_stdout command source in
   print_string result;
   [%expect{|
+    --- example/src/also-ignore-me/main.c
+    +++ example/src/also-ignore-me/main.c
+    @@ -1,1 +1,1 @@
+    -int main() {}
+    +int pain() {}
     --- example/src/honor-file-extensions/honor.pb.generic
     +++ example/src/honor-file-extensions/honor.pb.generic
     @@ -1,3 +1,3 @@
@@ -644,6 +650,11 @@ let%expect_test "matcher_override" =
   let result = read_expect_stdin_and_stdout command source in
   print_string result;
   [%expect{|
+    --- example/src/also-ignore-me/main.c
+    +++ example/src/also-ignore-me/main.c
+    @@ -1,1 +1,1 @@
+    -int main() {}
+    +int main_unbalanced_match_) {}
     --- example/src/ignore-me/main.c
     +++ example/src/ignore-me/main.c
     @@ -1,1 +1,1 @@
@@ -716,10 +727,10 @@ let%expect_test "diff_only" =
   [%expect{|
     -json-only-diff can only be supplied with -json-lines. |}]
 
-let%expect_test "zip_exclude_dir_with_extension" =
+let%expect_test "zip_exclude_dir_with_multiple_extension" =
   let source = "doesn't matter" in
   let zip = "example" ^/ "zip-test" ^/ "sample-repo.zip" in
-  let exclude_dir = "sample-repo/vendor" in
+  let exclude_dir = "sample-repo/vendor,sample-repo/ignore-this" in
   let command_args = Format.sprintf "'main' 'pain' .go -zip %s -sequential -diff -exclude-dir %s" zip exclude_dir in
   let command = Format.sprintf "%s %s" binary_path command_args in
   let result = read_expect_stdin_and_stdout command source in
@@ -735,7 +746,7 @@ let%expect_test "zip_exclude_dir_with_extension" =
 let%expect_test "zip_exclude_dir_no_extension" =
   let source = "doesn't matter" in
   let zip = "example" ^/ "zip-test" ^/ "sample-repo.zip" in
-  let exclude_dir = "sample-repo/vendor" in
+  let exclude_dir = "sample-repo/vendor,sample-repo/ignore-this" in
   let command_args = Format.sprintf "'main' 'pain' -zip %s -sequential -diff -exclude-dir %s" zip exclude_dir in
   let command = Format.sprintf "%s %s" binary_path command_args in
   let result = read_expect_stdin_and_stdout command source in
diff --git a/test/common/test_pipeline.ml b/test/common/test_pipeline.ml
index ab909b1b..4058a1f6 100644
--- a/test/common/test_pipeline.ml
+++ b/test/common/test_pipeline.ml
@@ -10,7 +10,7 @@ let matcher = (module Generic : Matchers.Matcher)
 let configuration =
   { sources = `String "source"
   ; specifications = []
-  ; exclude_directory_prefix = "."
+  ; exclude_directory_prefix = ["."]
   ; file_filters = None
   ; run_options =
       { sequential = true
diff --git a/test/example/src/also-ignore-me/main.c b/test/example/src/also-ignore-me/main.c
new file mode 100644
index 00000000..237c8ce1
--- /dev/null
+++ b/test/example/src/also-ignore-me/main.c
@@ -0,0 +1 @@
+int main() {}
diff --git a/test/example/zip-test/sample-repo.zip b/test/example/zip-test/sample-repo.zip
index 258ab6b0..dd3dd7dd 100644
Binary files a/test/example/zip-test/sample-repo.zip and b/test/example/zip-test/sample-repo.zip differ
diff --git a/test/example/zip-test/sample-repo/ignore-this/main.go b/test/example/zip-test/sample-repo/ignore-this/main.go
new file mode 100644
index 00000000..4a31737d
--- /dev/null
+++ b/test/example/zip-test/sample-repo/ignore-this/main.go
@@ -0,0 +1,2 @@
+// ignore-this
+func main() {}