diff --git a/app/services/delete_merged_branches_service.rb b/app/services/delete_merged_branches_service.rb
index 3b611588466..5c9e2a16c71 100644
--- a/app/services/delete_merged_branches_service.rb
+++ b/app/services/delete_merged_branches_service.rb
@@ -10,6 +10,8 @@ class DeleteMergedBranchesService < BaseService
     branches = branches.select { |branch| project.repository.merged_to_root_ref?(branch) }
     # Prevent deletion of branches relevant to open merge requests
     branches -= merge_request_branch_names
+    # Prevent deletion of protected branches
+    branches -= project.protected_branches.pluck(:name)
 
     branches.each do |branch|
       DeleteBranchService.new(project, current_user).execute(branch)
diff --git a/changelogs/unreleased/tc-no-delete-protected-merged-branches.yml b/changelogs/unreleased/tc-no-delete-protected-merged-branches.yml
new file mode 100644
index 00000000000..663a0349bac
--- /dev/null
+++ b/changelogs/unreleased/tc-no-delete-protected-merged-branches.yml
@@ -0,0 +1,4 @@
+---
+title: Do not delete protected branches when deleting all merged branches
+merge_request: 12624
+author:
diff --git a/spec/services/delete_merged_branches_service_spec.rb b/spec/services/delete_merged_branches_service_spec.rb
index cae74df9c90..fe21ca0b3cb 100644
--- a/spec/services/delete_merged_branches_service_spec.rb
+++ b/spec/services/delete_merged_branches_service_spec.rb
@@ -24,6 +24,14 @@ describe DeleteMergedBranchesService, services: true do
       expect(project.repository.branch_names).to include('master')
     end
 
+    it 'keeps protected branches' do
+      create(:protected_branch, project: project, name: 'improve/awesome')
+
+      service.execute
+
+      expect(project.repository.branch_names).to include('improve/awesome')
+    end
+
     context 'user without rights' do
       let(:user) { create(:user) }