diff --git a/app/models/pool_repository.rb b/app/models/pool_repository.rb
index 78cddaa13022881316cb4d96f2428a80441bbeee..3461104ae357d0fdb3331ed999faac21b1ddde88 100644
--- a/app/models/pool_repository.rb
+++ b/app/models/pool_repository.rb
@@ -81,7 +81,9 @@ def link_repository(repository)
     object_pool.link(repository.raw)
   end
 
-  def mark_obsolete_if_last(repository)
+  def unlink_repository(repository)
+    repository.disconnect_alternates
+
     if member_projects.where.not(id: repository.project.id).exists?
       true
     else
diff --git a/app/models/project.rb b/app/models/project.rb
index a215ff2a8781c6a08b1d518ef844b2eb2f46b6a9..6fadc207a29b6df6ea0cd1f5a71c019404087d73 100644
--- a/app/models/project.rb
+++ b/app/models/project.rb
@@ -2566,7 +2566,7 @@ def git_objects_poolable?
   end
 
   def leave_pool_repository
-    pool_repository&.mark_obsolete_if_last(repository) && update_column(:pool_repository_id, nil)
+    pool_repository&.unlink_repository(repository) && update_column(:pool_repository_id, nil)
   end
 
   def link_pool_repository
diff --git a/spec/models/pool_repository_spec.rb b/spec/models/pool_repository_spec.rb
index 92b3e41cd18cc0d8d35ed37ab374128601013f13..447b7b2e0a2c5310e96397a1854fc507cb4bfea3 100644
--- a/spec/models/pool_repository_spec.rb
+++ b/spec/models/pool_repository_spec.rb
@@ -24,23 +24,35 @@
     end
   end
 
-  describe '#mark_obsolete_if_last' do
+  describe '#unlink_repository' do
     let(:pool) { create(:pool_repository, :ready) }
+    let(:repository_path) { File.join(TestEnv.repos_path, pool.source_project.repository.relative_path) }
+    let(:alternates_file) { File.join(repository_path, 'objects', 'info', 'alternates') }
+
+    before do
+      pool.link_repository(pool.source_project.repository)
+    end
 
     context 'when the last member leaves' do
       it 'schedules pool removal' do
         expect(::ObjectPool::DestroyWorker).to receive(:perform_async).with(pool.id).and_call_original
 
-        pool.mark_obsolete_if_last(pool.source_project.repository)
+        pool.unlink_repository(pool.source_project.repository)
+
+        expect(File).not_to exist(alternates_file)
       end
     end
 
     context 'when the second member leaves' do
       it 'does not schedule pool removal' do
-        create(:project, :repository, pool_repository: pool)
+        other_project = create(:project, :repository, pool_repository: pool)
+        pool.link_repository(other_project.repository)
+
         expect(::ObjectPool::DestroyWorker).not_to receive(:perform_async).with(pool.id)
 
-        pool.mark_obsolete_if_last(pool.source_project.repository)
+        pool.unlink_repository(pool.source_project.repository)
+
+        expect(File).not_to exist(alternates_file)
       end
     end
   end