diff --git a/apps/emqx_ft/src/emqx_ft_storage_fs_gc.erl b/apps/emqx_ft/src/emqx_ft_storage_fs_gc.erl
index 20e4f468d..eb274a4d5 100644
--- a/apps/emqx_ft/src/emqx_ft_storage_fs_gc.erl
+++ b/apps/emqx_ft/src/emqx_ft_storage_fs_gc.erl
@@ -169,7 +169,7 @@ try_collect_transfer(Storage, Transfer, TransferInfo = #{}, Stats) ->
     % TODO: collect empty directories separately
     case FragCleaned and TempCleaned of
         true ->
-            collect_transfer_directory(Storage, Transfer, Stats2);
+            collect_transfer_directory(Storage, Transfer, Cutoff, Stats2);
         false ->
             Stats2
     end;
@@ -191,18 +191,32 @@ collect_tempfiles(Storage, Transfer, Stats) ->
 
 collect_outdated_fragments(Storage, Transfer, Cutoff, Stats) ->
     Dirname = emqx_ft_storage_fs:get_subdir(Storage, Transfer, fragment),
-    Filter = fun(_Filepath, #file_info{mtime = ModifiedAt}) -> ModifiedAt < Cutoff end,
-    maybe_collect_directory(Dirname, Filter, Stats).
+    maybe_collect_directory(Dirname, filter_older_than(Cutoff), Stats).
 
 collect_outdated_tempfiles(Storage, Transfer, Cutoff, Stats) ->
     Dirname = emqx_ft_storage_fs:get_subdir(Storage, Transfer, temporary),
-    Filter = fun(_Filepath, #file_info{mtime = ModifiedAt}) -> ModifiedAt < Cutoff end,
-    maybe_collect_directory(Dirname, Filter, Stats).
+    maybe_collect_directory(Dirname, filter_older_than(Cutoff), Stats).
 
-collect_transfer_directory(Storage, Transfer, Stats) ->
+collect_transfer_directory(Storage, Transfer, Cutoff, Stats) ->
     Dirname = emqx_ft_storage_fs:get_subdir(Storage, Transfer),
-    StatsNext = collect_empty_directory(Dirname, Stats),
-    collect_parents(Dirname, get_storage_root(Storage), StatsNext).
+    Filter =
+        case Stats of
+            #gcstats{directories = 0} ->
+                % Nothing were collected, this is a leftover from a past complete transfer GC.
+                filter_older_than(Cutoff);
+            #gcstats{} ->
+                % Usual incomplete transfer GC, collect directories unconditionally.
+                true
+        end,
+    case collect_empty_directory(Dirname, Filter, Stats) of
+        {true, StatsNext} ->
+            collect_parents(Dirname, get_storage_root(Storage), StatsNext);
+        {false, StatsNext} ->
+            StatsNext
+    end.
+
+filter_older_than(Cutoff) ->
+    fun(_Filepath, #file_info{mtime = ModifiedAt}) -> ModifiedAt =< Cutoff end.
 
 collect_parents(Dirname, Until, Stats) ->
     Parent = filename:dirname(Dirname),
@@ -218,14 +232,6 @@ collect_parents(Dirname, Until, Stats) ->
             register_gcstat_error({directory, Parent}, Reason, Stats)
     end.
 
-% collect_outdated_fragment(#{path := Filepath, fileinfo := Fileinfo}, Cutoff, Stats) ->
-%     case Fileinfo#file_info.mtime of
-%         ModifiedAt when ModifiedAt < Cutoff ->
-%             collect_filepath(Filepath, Fileinfo, Stats);
-%         _ ->
-%             Stats
-%     end.
-
 maybe_collect_directory(Dirpath, Filter, Stats) ->
     case filelib:is_dir(Dirpath) of
         true ->
@@ -263,10 +269,10 @@ collect_directory(Dirpath, Fileinfo, Filter, Stats) ->
     case file:list_dir(Dirpath) of
         {ok, Filenames} ->
             {Clean, StatsNext} = collect_files(Dirpath, Filenames, Filter, Stats),
-            case Clean andalso filter_filepath(Filter, Dirpath, Fileinfo) of
+            case Clean of
                 true ->
-                    {true, collect_empty_directory(Dirpath, StatsNext)};
-                _ ->
+                    collect_empty_directory(Dirpath, Fileinfo, Filter, StatsNext);
+                false ->
                     {false, StatsNext}
             end;
         {error, Reason} ->
@@ -284,13 +290,23 @@ collect_files(Dirname, Filenames, Filter, Stats) ->
         Filenames
     ).
 
-collect_empty_directory(Dirpath, Stats) ->
-    case file:del_dir(Dirpath) of
+collect_empty_directory(Dirpath, Filter, Stats) ->
+    case file:read_link_info(Dirpath, [{time, posix}, raw]) of
+        {ok, Dirinfo} ->
+            collect_empty_directory(Dirpath, Dirinfo, Filter, Stats);
+        {error, Reason} ->
+            {Reason == enoent, register_gcstat_error({directory, Dirpath}, Reason, Stats)}
+    end.
+
+collect_empty_directory(Dirpath, Dirinfo, Filter, Stats) ->
+    case filter_filepath(Filter, Dirpath, Dirinfo) andalso file:del_dir(Dirpath) of
+        false ->
+            {false, Stats};
         ok ->
             ?tp(garbage_collected_directory, #{path => Dirpath}),
-            account_gcstat_directory(Stats);
+            {true, account_gcstat_directory(Stats)};
         {error, Reason} ->
-            register_gcstat_error({directory, Dirpath}, Reason, Stats)
+            {false, register_gcstat_error({directory, Dirpath}, Reason, Stats)}
     end.
 
 filter_filepath(Filter, _, _) when is_boolean(Filter) ->
diff --git a/apps/emqx_ft/test/emqx_ft_storage_fs_gc_SUITE.erl b/apps/emqx_ft/test/emqx_ft_storage_fs_gc_SUITE.erl
index 25cd200f1..53a22b8b6 100644
--- a/apps/emqx_ft/test/emqx_ft_storage_fs_gc_SUITE.erl
+++ b/apps/emqx_ft/test/emqx_ft_storage_fs_gc_SUITE.erl
@@ -104,6 +104,10 @@ t_gc_triggers_manually(_Config) ->
 
 t_gc_complete_transfers(_Config) ->
     Storage = emqx_ft_conf:storage(),
+    ok = emqx_config:put([file_transfer, storage, gc, minimum_segments_ttl], 0),
+    ok = emqx_config:put([file_transfer, storage, gc, maximum_segments_ttl], 3),
+    ok = emqx_config:put([file_transfer, storage, gc, interval], 500),
+    ok = emqx_ft_storage_fs_gc:reset(Storage),
     Transfers = [
         {
             T1 = {<<"client1">>, mk_file_id()},
@@ -174,7 +178,20 @@ t_gc_complete_transfers(_Config) ->
     ?assertEqual(?NSEGS(S2, SS2) + ?NSEGS(S3, SS3), CFiles),
     ?assertEqual(2 + 2, CDirectories),
     ?assertMatch(Space when Space > S2 + S3, CSpace),
-    ?assertMatch(Errors when map_size(Errors) == 0, CErrors).
+    ?assertMatch(Errors when map_size(Errors) == 0, CErrors),
+    % 4. Ensure that empty transfer directories will be eventually collected
+    {ok, _} = ?block_until(
+        #{
+            ?snk_kind := garbage_collection,
+            stats := #gcstats{
+                files = 0,
+                directories = 6,
+                space = 0
+            }
+        },
+        5000,
+        0
+    ).
 
 t_gc_incomplete_transfers(_Config) ->
     ok = emqx_config:put([file_transfer, storage, gc, minimum_segments_ttl], 0),