diff --git a/db/post_migrate/20170526101042_migrate_pipeline_stages.rb b/db/post_migrate/20170526101042_migrate_pipeline_stages.rb
index fdbefd59edf..05e095f07cb 100644
--- a/db/post_migrate/20170526101042_migrate_pipeline_stages.rb
+++ b/db/post_migrate/20170526101042_migrate_pipeline_stages.rb
@@ -15,14 +15,6 @@ class MigratePipelineStages < ActiveRecord::Migration
           GROUP BY project_id, commit_id, stage, stage_idx
           ORDER BY stage_idx
     SQL
-
-    stage_id = Arel.sql('(SELECT id FROM ci_stages ' \
-                         'WHERE ci_stages.pipeline_id = ci_builds.commit_id ' \
-                         'AND ci_stages.name = ci_builds.stage)')
-    update_column_in_batches(:ci_builds, :stage_id, stage_id)
-
-    # add_concurrent_foreign_key :ci_stages, :projects, column: :project_id, on_delete: :cascade
-    # add_concurrent_foreign_key :ci_builds, :ci_stages, column: :stage_id, on_delete: :cascade
   end
 
   def down
diff --git a/db/post_migrate/20170526185921_migrate_build_stage_reference.rb b/db/post_migrate/20170526185921_migrate_build_stage_reference.rb
new file mode 100644
index 00000000000..8f453b8cd82
--- /dev/null
+++ b/db/post_migrate/20170526185921_migrate_build_stage_reference.rb
@@ -0,0 +1,21 @@
+class MigrateBuildStageReference < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+
+  def up
+    disable_statement_timeout
+
+    stage_id = Arel.sql('(SELECT id FROM ci_stages ' \
+                         'WHERE ci_stages.pipeline_id = ci_builds.commit_id ' \
+                         'AND ci_stages.name = ci_builds.stage)')
+
+    update_column_in_batches(:ci_builds, :stage_id, stage_id)
+  end
+
+  def down
+    disable_statement_timeout
+
+    update_column_in_batches(:ci_builds, :stage_id, nil)
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index f1df8d6bd8c..87e16e2f69c 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -11,7 +11,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20170526101042) do
+ActiveRecord::Schema.define(version: 20170526185921) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
diff --git a/spec/migrations/migrate_build_stage_reference_spec.rb b/spec/migrations/migrate_build_stage_reference_spec.rb
new file mode 100644
index 00000000000..979f13a1398
--- /dev/null
+++ b/spec/migrations/migrate_build_stage_reference_spec.rb
@@ -0,0 +1,56 @@
+require 'spec_helper'
+require Rails.root.join('db', 'post_migrate', '20170526185921_migrate_build_stage_reference.rb')
+
+describe MigrateBuildStageReference, :migration, schema: 20170526185602 do
+  ##
+  # Create test data - pipeline and CI/CD jobs.
+  #
+
+  let(:jobs) { table(:ci_builds) }
+  let(:stages) { table(:ci_stages) }
+  let(:pipelines) { table(:ci_pipelines) }
+
+  before do
+    # Create CI/CD pipelines
+    #
+    pipelines.create!(id: 1, project_id: 123, ref: 'master', sha: 'adf43c3a')
+    pipelines.create!(id: 2, project_id: 456, ref: 'feature', sha: '21a3deb')
+
+    # Create CI/CD jobs
+    #
+    jobs.create!(id: 1, commit_id: 1, project_id: 123, stage_idx: 2, stage: 'build')
+    jobs.create!(id: 2, commit_id: 1, project_id: 123, stage_idx: 2, stage: 'build')
+    jobs.create!(id: 3, commit_id: 1, project_id: 123, stage_idx: 1, stage: 'test')
+    jobs.create!(id: 4, commit_id: 1, project_id: 123, stage_idx: 3, stage: 'deploy')
+    jobs.create!(id: 5, commit_id: 2, project_id: 456, stage_idx: 2, stage: 'test:2')
+    jobs.create!(id: 6, commit_id: 2, project_id: 456, stage_idx: 1, stage: 'test:1')
+    jobs.create!(id: 7, commit_id: 2, project_id: 456, stage_idx: 1, stage: 'test:1')
+    jobs.create!(id: 8, commit_id: 3, project_id: 789, stage_idx: 3, stage: 'deploy')
+
+    # Create CI/CD stages
+    #
+    stages.create(id: 101, pipeline_id: 1, project_id: 123, name: 'test')
+    stages.create(id: 102, pipeline_id: 1, project_id: 123, name: 'build')
+    stages.create(id: 103, pipeline_id: 1, project_id: 123, name: 'deploy')
+    stages.create(id: 104, pipeline_id: 2, project_id: 456, name: 'test:1')
+    stages.create(id: 105, pipeline_id: 2, project_id: 456, name: 'test:2')
+    stages.create(id: 106, pipeline_id: 2, project_id: 456, name: 'deploy')
+  end
+
+  it 'correctly migrate build stage references' do
+    expect(jobs.where(stage_id: nil).count).to eq 8
+
+    migrate!
+
+    expect(jobs.where(stage_id: nil).count).to eq 1
+
+    expect(jobs.find(1).stage_id).to eq 102
+    expect(jobs.find(2).stage_id).to eq 102
+    expect(jobs.find(3).stage_id).to eq 101
+    expect(jobs.find(4).stage_id).to eq 103
+    expect(jobs.find(5).stage_id).to eq 105
+    expect(jobs.find(6).stage_id).to eq 104
+    expect(jobs.find(7).stage_id).to eq 104
+    expect(jobs.find(8).stage_id).to eq nil
+  end
+end
diff --git a/spec/migrations/migrate_pipeline_stages_spec.rb b/spec/migrations/migrate_pipeline_stages_spec.rb
index 9cf13a1dabc..6887fcd26c3 100644
--- a/spec/migrations/migrate_pipeline_stages_spec.rb
+++ b/spec/migrations/migrate_pipeline_stages_spec.rb
@@ -43,7 +43,5 @@ describe MigratePipelineStages, :migration, schema: 20170525132202 do
       .to eq %w[test build deploy]
     expect(stages.where(pipeline_id: 2).order(:id).pluck(:name))
       .to eq %w[test:1 test:2 deploy]
-
-    expect(jobs.where(stage_id: nil)).to be_empty
   end
 end