diff --git a/app/models/merge_request.rb b/app/models/merge_request.rb
index 98f1931ce5ea02c72f55596819098ed0a9a371d1..b8eca3def022e5604bed178a8ce64547b87a0006 100644
--- a/app/models/merge_request.rb
+++ b/app/models/merge_request.rb
@@ -1904,13 +1904,7 @@ def rebase_on_merge_path
   end
 
   def schedule_cleanup_refs(only: :all)
-    if Feature.enabled?(:merge_request_delete_gitaly_refs_in_batches, target_project)
-      async_cleanup_refs(only: only)
-    elsif Feature.enabled?(:merge_request_cleanup_ref_worker_async, target_project)
-      MergeRequests::CleanupRefWorker.perform_async(id, only.to_s)
-    else
-      cleanup_refs(only: only)
-    end
+    async_cleanup_refs(only: only)
   end
 
   def refs_to_cleanup(only: :all)
diff --git a/config/feature_flags/development/merge_request_delete_gitaly_refs_in_batches.yml b/config/feature_flags/development/merge_request_delete_gitaly_refs_in_batches.yml
deleted file mode 100644
index 0f0b81dbbd281bd7cf09141e693faefe6a8e798f..0000000000000000000000000000000000000000
--- a/config/feature_flags/development/merge_request_delete_gitaly_refs_in_batches.yml
+++ /dev/null
@@ -1,8 +0,0 @@
----
-name: merge_request_delete_gitaly_refs_in_batches
-introduced_by_url: https://gitlab.com/gitlab-org/gitlab/-/merge_requests/125333
-rollout_issue_url: https://gitlab.com/gitlab-org/gitlab/-/issues/416969
-milestone: '16.3'
-type: development
-group: group::gitaly
-default_enabled: false
diff --git a/doc/user/project/repository/monorepos/troubleshooting.md b/doc/user/project/repository/monorepos/troubleshooting.md
index 769a6094caa44ffa916d756957993bf7d0edb736..ae627a6fa13cbaa23b9d7325c22027779ef61b4f 100644
--- a/doc/user/project/repository/monorepos/troubleshooting.md
+++ b/doc/user/project/repository/monorepos/troubleshooting.md
@@ -91,7 +91,8 @@ These feature flags do not need downtime to enable.
 - `merge_request_cleanup_ref_worker_async`
 - `pipeline_cleanup_ref_worker_async`
 - `pipeline_delete_gitaly_refs_in_batches`
-- `merge_request_delete_gitaly_refs_in_batches`
+
+> - [Generally available](https://gitlab.com/gitlab-org/gitlab/-/issues/416969) in GitLab 18.5. Feature flag `merge_request_delete_gitaly_refs_in_batches` removed.
 
 [Epic 4220](https://gitlab.com/groups/gitlab-org/-/epics/4220) proposes to add RefTable support in GitLab,
 which is considered a long-term solution.
diff --git a/ee/app/models/merge_trains/car.rb b/ee/app/models/merge_trains/car.rb
index b6cb59c1d5eaf6d0c0468984c2592ef09e5948ea..87f839f96eada02e25686a2d6672d429222c77f6 100644
--- a/ee/app/models/merge_trains/car.rb
+++ b/ee/app/models/merge_trains/car.rb
@@ -179,8 +179,7 @@ def first_car?
 
     def try_cleanup_ref(async: true)
       # The async variant isn't necessarily async, it depends on the feature
-      # flags merge_request_delete_gitaly_refs_in_batches and
-      # merge_request_cleanup_ref_worker_async
+      # flag merge_request_cleanup_ref_worker_async
       cleanup_ref(async: async)
     rescue ::Gitlab::Git::BaseError => e
       Gitlab::ErrorTracking.track_exception(e)
diff --git a/spec/models/merge_request_spec.rb b/spec/models/merge_request_spec.rb
index dbe3bb4ab407d43a2402f3b2aea34691fa1a6ed3..0e95a7ba5ce137f974826ea19b08b7e8bc8ed74f 100644
--- a/spec/models/merge_request_spec.rb
+++ b/spec/models/merge_request_spec.rb
@@ -6164,30 +6164,25 @@ def transition!
       subject
     end
 
-    context 'when merge_request_delete_gitaly_refs_in_batches is disabled' do
-      before do
-        stub_feature_flags(merge_request_delete_gitaly_refs_in_batches: false)
-      end
+    it 'deletes refs asynchronously' do
+      expect(merge_request.target_project.repository)
+        .to receive(:async_delete_refs)
+        .with(merge_request.train_ref_path)
 
-      it 'does schedule MergeRequests::CleanupRefWorker' do
-        expect(MergeRequests::CleanupRefWorker).to receive(:perform_async).with(merge_request.id, 'train')
+      subject
+    end
 
-        subject
+    context 'when merge_request_cleanup_ref_worker_async is disabled' do
+      before do
+        stub_feature_flags(merge_request_cleanup_ref_worker_async: false)
       end
 
-      context 'when merge_request_cleanup_ref_worker_async is disabled' do
-        before do
-          stub_feature_flags(merge_request_delete_gitaly_refs_in_batches: false)
-          stub_feature_flags(merge_request_cleanup_ref_worker_async: false)
-        end
-
-        it 'deletes all refs from the target project' do
-          expect(merge_request.target_project.repository)
-            .to receive(:delete_refs)
-            .with(merge_request.train_ref_path)
+      it 'deletes all refs from the target project' do
+        expect(merge_request.target_project.repository)
+          .to receive(:delete_refs)
+          .with(merge_request.train_ref_path)
 
-          subject
-        end
+        subject
       end
     end
   end
diff --git a/spec/services/merge_requests/cleanup_refs_service_spec.rb b/spec/services/merge_requests/cleanup_refs_service_spec.rb
index a80a29b220abc32c44df2de3a93ca3e6f55cacf7..404f8b27c3bebb601fab204397f4f904d581481d 100644
--- a/spec/services/merge_requests/cleanup_refs_service_spec.rb
+++ b/spec/services/merge_requests/cleanup_refs_service_spec.rb
@@ -18,7 +18,6 @@
 
   describe '#execute' do
     before do
-      stub_feature_flags(merge_request_delete_gitaly_refs_in_batches: false)
       stub_feature_flags(merge_request_cleanup_ref_worker_async: false)
 
       merge_request.create_cleanup_schedule(scheduled_at: described_class::TIME_THRESHOLD.ago)