diff --git a/app/services/ci/pipelines/clear_persistent_ref_service.rb b/app/services/ci/pipelines/clear_persistent_ref_service.rb
index a3980d5905590cf26ce25180b2205abe72bebbfc..c2e4928e59154e2e35d6c11b4b515acafaf4e493 100644
--- a/app/services/ci/pipelines/clear_persistent_ref_service.rb
+++ b/app/services/ci/pipelines/clear_persistent_ref_service.rb
@@ -6,9 +6,7 @@ class ClearPersistentRefService < CreatePersistentRefService
       def execute
         Rails.cache.delete(pipeline_persistent_ref_cache_key)
 
-        if Feature.enabled?(:pipeline_delete_gitaly_refs_in_batches, pipeline.project)
-          pipeline.persistent_ref.async_delete
-        elsif Feature.enabled?(:pipeline_cleanup_ref_worker_async, pipeline.project)
+        if Feature.enabled?(:pipeline_cleanup_ref_worker_async, pipeline.project)
           ::Ci::PipelineCleanupRefWorker.perform_async(pipeline.id)
         else
           pipeline.persistent_ref.delete
diff --git a/config/feature_flags/development/pipeline_delete_gitaly_refs_in_batches.yml b/config/feature_flags/development/pipeline_delete_gitaly_refs_in_batches.yml
deleted file mode 100644
index 66e23fa424a3393e93f664a898f804ee6c79c62e..0000000000000000000000000000000000000000
--- a/config/feature_flags/development/pipeline_delete_gitaly_refs_in_batches.yml
+++ /dev/null
@@ -1,8 +0,0 @@
----
-name: pipeline_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..763d6ac492dccf139844a50178364a097fea3f88 100644
--- a/doc/user/project/repository/monorepos/troubleshooting.md
+++ b/doc/user/project/repository/monorepos/troubleshooting.md
@@ -90,8 +90,9 @@ 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 `pipeline_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/spec/models/ci/persistent_ref_spec.rb b/spec/models/ci/persistent_ref_spec.rb
index 9b3f9a8e094b99716fba0f937fdac4b9abd1cabc..edfc76376c0331ccb8b4d433eb528beb8298ee4d 100644
--- a/spec/models/ci/persistent_ref_spec.rb
+++ b/spec/models/ci/persistent_ref_spec.rb
@@ -11,32 +11,26 @@
       .by(1)
   end
 
-  context 'when pipeline_delete_gitaly_refs_in_batches is disabled' do
+  it 'cleans up persistent refs after pipeline finished' do
+    pipeline = create(:ci_pipeline, :running)
+
+    expect(Ci::PipelineCleanupRefWorker).to receive(:perform_async).with(pipeline.id)
+
+    pipeline.succeed!
+  end
+
+  context 'when pipeline_cleanup_ref_worker_async is disabled' do
     before do
-      stub_feature_flags(pipeline_delete_gitaly_refs_in_batches: false)
+      stub_feature_flags(pipeline_cleanup_ref_worker_async: false)
     end
 
     it 'cleans up persistent refs after pipeline finished' do
       pipeline = create(:ci_pipeline, :running)
 
-      expect(Ci::PipelineCleanupRefWorker).to receive(:perform_async).with(pipeline.id)
+      expect(pipeline.persistent_ref).to receive(:delete).once
 
       pipeline.succeed!
     end
-
-    context 'when pipeline_cleanup_ref_worker_async is disabled' do
-      before do
-        stub_feature_flags(pipeline_cleanup_ref_worker_async: false)
-      end
-
-      it 'cleans up persistent refs after pipeline finished' do
-        pipeline = create(:ci_pipeline, :running)
-
-        expect(pipeline.persistent_ref).to receive(:delete).once
-
-        pipeline.succeed!
-      end
-    end
   end
 
   describe '#exist?' do
diff --git a/spec/models/ci/pipeline_spec.rb b/spec/models/ci/pipeline_spec.rb
index 61d7ec4bad0f545509e37ef8ef10f28f6388f08b..6b0015c6b049924245c813ea882c9dc0023fd48a 100644
--- a/spec/models/ci/pipeline_spec.rb
+++ b/spec/models/ci/pipeline_spec.rb
@@ -1903,40 +1903,19 @@ def create_build(name, status)
           pipeline.public_send(action)
         end
 
-        context 'when pipeline_delete_gitaly_refs_in_batches is disabled' do
+        context 'when pipeline_cleanup_ref_worker_async is disabled' do
           before do
-            stub_feature_flags(pipeline_delete_gitaly_refs_in_batches: false)
+            stub_feature_flags(pipeline_cleanup_ref_worker_async: false)
           end
 
-          it 'deletes a persistent ref asynchronously via ::Ci::PipelineCleanupRefWorker', :sidekiq_inline do
-            expect(pipeline.persistent_ref).not_to receive(:delete_refs)
+          it 'deletes a persistent ref synchronously' do
+            expect(Ci::PipelineCleanupRefWorker).not_to receive(:perform_async).with(pipeline.id)
 
-            expect(Ci::PipelineCleanupRefWorker).to receive(:perform_async)
-              .with(pipeline.id).and_call_original
-
-            expect_next_instance_of(Ci::PersistentRef) do |persistent_ref|
-              expect(persistent_ref).to receive(:delete_refs)
-                .with("refs/#{Repository::REF_PIPELINES}/#{pipeline.id}").once
-            end
+            expect(pipeline.persistent_ref).to receive(:delete_refs).once
+              .with("refs/#{Repository::REF_PIPELINES}/#{pipeline.id}")
 
             pipeline.public_send(action)
           end
-
-          context 'when pipeline_cleanup_ref_worker_async is disabled' do
-            before do
-              stub_feature_flags(pipeline_delete_gitaly_refs_in_batches: false)
-              stub_feature_flags(pipeline_cleanup_ref_worker_async: false)
-            end
-
-            it 'deletes a persistent ref synchronously' do
-              expect(Ci::PipelineCleanupRefWorker).not_to receive(:perform_async).with(pipeline.id)
-
-              expect(pipeline.persistent_ref).to receive(:delete_refs).once
-                .with("refs/#{Repository::REF_PIPELINES}/#{pipeline.id}")
-
-              pipeline.public_send(action)
-            end
-          end
         end
       end
     end
diff --git a/spec/services/ci/pipelines/clear_persistent_ref_service_spec.rb b/spec/services/ci/pipelines/clear_persistent_ref_service_spec.rb
index 8216e39f9eff234b62abdade31668eb56447aa7a..7411c178c838add6565f132b3cc5e88cbd26e524 100644
--- a/spec/services/ci/pipelines/clear_persistent_ref_service_spec.rb
+++ b/spec/services/ci/pipelines/clear_persistent_ref_service_spec.rb
@@ -20,41 +20,34 @@
       .to change { Rails.cache.read(service.send(:pipeline_persistent_ref_cache_key)) }.from(true).to(nil)
   end
 
-  context 'when pipeline_delete_gitaly_refs_in_batches is disabled' do
-    before do
-      stub_feature_flags(pipeline_delete_gitaly_refs_in_batches: false)
-    end
+  it 'deletes a persistent ref asynchronously via ::Ci::PipelineCleanupRefWorker', :sidekiq_inline do
+    expect(pipeline.persistent_ref).not_to receive(:delete_refs)
 
-    it 'deletes a persistent ref asynchronously via ::Ci::PipelineCleanupRefWorker', :sidekiq_inline do
-      expect(pipeline.persistent_ref).not_to receive(:delete_refs)
+    expect(Ci::PipelineCleanupRefWorker).to receive(:perform_async)
+      .with(pipeline.id).and_call_original
 
-      expect(Ci::PipelineCleanupRefWorker).to receive(:perform_async)
-        .with(pipeline.id).and_call_original
+    expect_next_instance_of(Ci::PersistentRef) do |persistent_ref|
+      expect(persistent_ref).to receive(:delete_refs)
+        .with("refs/#{Repository::REF_PIPELINES}/#{pipeline.id}").once
+    end
 
-      expect_next_instance_of(Ci::PersistentRef) do |persistent_ref|
-        expect(persistent_ref).to receive(:delete_refs)
-          .with("refs/#{Repository::REF_PIPELINES}/#{pipeline.id}").once
-      end
+    expect { service.execute }
+      .to change { Rails.cache.read(service.send(:pipeline_persistent_ref_cache_key)) }.from(true).to(nil)
+  end
 
-      expect { service.execute }
-        .to change { Rails.cache.read(service.send(:pipeline_persistent_ref_cache_key)) }.from(true).to(nil)
+  context 'when pipeline_cleanup_ref_worker_async is disabled' do
+    before do
+      stub_feature_flags(pipeline_cleanup_ref_worker_async: false)
     end
 
-    context 'when pipeline_cleanup_ref_worker_async is disabled' do
-      before do
-        stub_feature_flags(pipeline_delete_gitaly_refs_in_batches: false)
-        stub_feature_flags(pipeline_cleanup_ref_worker_async: false)
-      end
+    it 'deletes a persistent ref synchronously' do
+      expect(Ci::PipelineCleanupRefWorker).not_to receive(:perform_async).with(pipeline.id)
 
-      it 'deletes a persistent ref synchronously' do
-        expect(Ci::PipelineCleanupRefWorker).not_to receive(:perform_async).with(pipeline.id)
+      expect(pipeline.persistent_ref).to receive(:delete_refs).once
+        .with("refs/#{Repository::REF_PIPELINES}/#{pipeline.id}")
 
-        expect(pipeline.persistent_ref).to receive(:delete_refs).once
-          .with("refs/#{Repository::REF_PIPELINES}/#{pipeline.id}")
-
-        expect { service.execute }
-          .to change { Rails.cache.read(service.send(:pipeline_persistent_ref_cache_key)) }.from(true).to(nil)
-      end
+      expect { service.execute }
+        .to change { Rails.cache.read(service.send(:pipeline_persistent_ref_cache_key)) }.from(true).to(nil)
     end
   end
 end