diff --git a/app/models/merge_request_diff.rb b/app/models/merge_request_diff.rb
index ec87aee9310..d9d746ccf41 100644
--- a/app/models/merge_request_diff.rb
+++ b/app/models/merge_request_diff.rb
@@ -85,11 +85,7 @@ class MergeRequestDiff < ActiveRecord::Base
 
   def raw_diffs(options = {})
     if options[:ignore_whitespace_change]
-      @diffs_no_whitespace ||=
-        Gitlab::Git::Compare.new(
-          repository.raw_repository,
-          safe_start_commit_sha,
-          head_commit_sha).diffs(options)
+      @diffs_no_whitespace ||= compare.diffs(options)
     else
       @raw_diffs ||= {}
       @raw_diffs[options] ||= load_diffs(options)
diff --git a/db/post_migrate/20170703130158_schedule_merge_request_diff_migrations.rb b/db/post_migrate/20170703130158_schedule_merge_request_diff_migrations.rb
new file mode 100644
index 00000000000..17a9dc293f1
--- /dev/null
+++ b/db/post_migrate/20170703130158_schedule_merge_request_diff_migrations.rb
@@ -0,0 +1,33 @@
+class ScheduleMergeRequestDiffMigrations < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+  BATCH_SIZE = 2500
+  MIGRATION = 'DeserializeMergeRequestDiffsAndCommits'
+
+  disable_ddl_transaction!
+
+  class MergeRequestDiff < ActiveRecord::Base
+    self.table_name = 'merge_request_diffs'
+
+    include ::EachBatch
+  end
+
+  # Assuming that there are 5 million rows affected (which is more than on
+  # GitLab.com), and that each batch of 2,500 rows takes up to 5 minutes, then
+  # we can migrate all the rows in 7 days.
+  #
+  # On staging, plucking the IDs themselves takes 5 seconds.
+  def up
+    non_empty = 'st_commits IS NOT NULL OR st_diffs IS NOT NULL'
+
+    MergeRequestDiff.where(non_empty).each_batch(of: BATCH_SIZE) do |relation, index|
+      range = relation.pluck('MIN(id)', 'MAX(id)').first
+
+      BackgroundMigrationWorker.perform_in(index * 5.minutes, MIGRATION, range)
+    end
+  end
+
+  def down
+  end
+end
diff --git a/lib/gitlab/background_migration/deserialize_merge_request_diffs_and_commits.rb b/lib/gitlab/background_migration/deserialize_merge_request_diffs_and_commits.rb
new file mode 100644
index 00000000000..0fbc6b70989
--- /dev/null
+++ b/lib/gitlab/background_migration/deserialize_merge_request_diffs_and_commits.rb
@@ -0,0 +1,107 @@
+module Gitlab
+  module BackgroundMigration
+    class DeserializeMergeRequestDiffsAndCommits
+      attr_reader :diff_ids, :commit_rows, :file_rows
+
+      class MergeRequestDiff < ActiveRecord::Base
+        self.table_name = 'merge_request_diffs'
+      end
+
+      BUFFER_ROWS = 1000
+
+      def perform(start_id, stop_id)
+        merge_request_diffs = MergeRequestDiff
+                               .select(:id, :st_commits, :st_diffs)
+                               .where('st_commits IS NOT NULL OR st_diffs IS NOT NULL')
+                               .where(id: start_id..stop_id)
+
+        reset_buffers!
+
+        merge_request_diffs.each do |merge_request_diff|
+          commits, files = single_diff_rows(merge_request_diff)
+
+          diff_ids << merge_request_diff.id
+          commit_rows.concat(commits)
+          file_rows.concat(files)
+
+          if diff_ids.length > BUFFER_ROWS ||
+              commit_rows.length > BUFFER_ROWS ||
+              file_rows.length > BUFFER_ROWS
+
+            flush_buffers!
+          end
+        end
+
+        flush_buffers!
+      end
+
+      private
+
+      def reset_buffers!
+        @diff_ids = []
+        @commit_rows = []
+        @file_rows = []
+      end
+
+      def flush_buffers!
+        if diff_ids.any?
+          MergeRequestDiff.transaction do
+            Gitlab::Database.bulk_insert('merge_request_diff_commits', commit_rows)
+            Gitlab::Database.bulk_insert('merge_request_diff_files', file_rows)
+
+            MergeRequestDiff.where(id: diff_ids).update_all(st_commits: nil, st_diffs: nil)
+          end
+        end
+
+        reset_buffers!
+      end
+
+      def single_diff_rows(merge_request_diff)
+        sha_attribute = Gitlab::Database::ShaAttribute.new
+        commits = YAML.load(merge_request_diff.st_commits) rescue []
+
+        commit_rows = commits.map.with_index do |commit, index|
+          commit_hash = commit.to_hash.with_indifferent_access.except(:parent_ids)
+          sha = commit_hash.delete(:id)
+
+          commit_hash.merge(
+            merge_request_diff_id: merge_request_diff.id,
+            relative_order: index,
+            sha: sha_attribute.type_cast_for_database(sha)
+          )
+        end
+
+        diffs = YAML.load(merge_request_diff.st_diffs) rescue []
+        diffs = [] unless valid_raw_diffs?(diffs)
+
+        file_rows = diffs.map.with_index do |diff, index|
+          diff_hash = diff.to_hash.with_indifferent_access.merge(
+            binary: false,
+            merge_request_diff_id: merge_request_diff.id,
+            relative_order: index
+          )
+
+          # Compatibility with old diffs created with Psych.
+          diff_hash.tap do |hash|
+            diff_text = hash[:diff]
+
+            if diff_text.encoding == Encoding::BINARY && !diff_text.ascii_only?
+              hash[:binary] = true
+              hash[:diff] = [diff_text].pack('m0')
+            end
+          end
+        end
+
+        [commit_rows, file_rows]
+      end
+
+      # Unlike MergeRequestDiff#valid_raw_diff?, don't count Rugged objects as
+      # valid, because we don't render them usefully anyway.
+      def valid_raw_diffs?(diffs)
+        return false unless diffs.respond_to?(:each)
+
+        diffs.all? { |diff| diff.is_a?(Hash) }
+      end
+    end
+  end
+end
diff --git a/spec/lib/gitlab/background_migration/deserialize_merge_request_diffs_and_commits_spec.rb b/spec/lib/gitlab/background_migration/deserialize_merge_request_diffs_and_commits_spec.rb
new file mode 100644
index 00000000000..18843cbe992
--- /dev/null
+++ b/spec/lib/gitlab/background_migration/deserialize_merge_request_diffs_and_commits_spec.rb
@@ -0,0 +1,188 @@
+require 'spec_helper'
+
+describe Gitlab::BackgroundMigration::DeserializeMergeRequestDiffsAndCommits do
+  describe '#perform' do
+    set(:merge_request) { create(:merge_request) }
+    set(:merge_request_diff) { merge_request.merge_request_diff }
+    let(:updated_merge_request_diff) { MergeRequestDiff.find(merge_request_diff.id) }
+
+    def diffs_to_hashes(diffs)
+      diffs.as_json(only: Gitlab::Git::Diff::SERIALIZE_KEYS).map(&:with_indifferent_access)
+    end
+
+    def quote_yaml(value)
+      MergeRequestDiff.connection.quote(YAML.dump(value))
+    end
+
+    def convert_to_yaml(merge_request_diff_id, commits, diffs)
+      MergeRequestDiff.where(id: merge_request_diff_id).update_all(
+        "st_commits = #{quote_yaml(commits)}, st_diffs = #{quote_yaml(diffs)}"
+      )
+    end
+
+    shared_examples 'updated MR diff' do
+      before do
+        convert_to_yaml(merge_request_diff.id, commits, diffs)
+
+        MergeRequestDiffCommit.delete_all
+        MergeRequestDiffFile.delete_all
+
+        subject.perform(merge_request_diff.id, merge_request_diff.id)
+      end
+
+      it 'creates correct entries in the merge_request_diff_commits table' do
+        expect(updated_merge_request_diff.merge_request_diff_commits.count).to eq(commits.count)
+        expect(updated_merge_request_diff.commits.map(&:to_hash)).to eq(commits)
+      end
+
+      it 'creates correct entries in the merge_request_diff_files table' do
+        expect(updated_merge_request_diff.merge_request_diff_files.count).to eq(expected_diffs.count)
+        expect(diffs_to_hashes(updated_merge_request_diff.raw_diffs)).to eq(expected_diffs)
+      end
+
+      it 'sets the st_commits and st_diffs columns to nil' do
+        expect(updated_merge_request_diff.st_commits_before_type_cast).to be_nil
+        expect(updated_merge_request_diff.st_diffs_before_type_cast).to be_nil
+      end
+    end
+
+    context 'when the diff IDs passed do not exist' do
+      it 'does not raise' do
+        expect { subject.perform(0, 0) }.not_to raise_exception
+      end
+    end
+
+    context 'when the merge request diff has no serialised commits or diffs' do
+      before do
+        merge_request_diff.update(st_commits: nil, st_diffs: nil)
+      end
+
+      it 'does not raise' do
+        expect { subject.perform(merge_request_diff.id, merge_request_diff.id) }
+          .not_to raise_exception
+      end
+    end
+
+    context 'processing multiple merge request diffs' do
+      let(:start_id) { described_class::MergeRequestDiff.minimum(:id) }
+      let(:stop_id) { described_class::MergeRequestDiff.maximum(:id) }
+
+      before do
+        merge_request.reload_diff(true)
+
+        convert_to_yaml(start_id, merge_request_diff.commits, merge_request_diff.diffs)
+        convert_to_yaml(stop_id, updated_merge_request_diff.commits, updated_merge_request_diff.diffs)
+
+        MergeRequestDiffCommit.delete_all
+        MergeRequestDiffFile.delete_all
+      end
+
+      context 'when BUFFER_ROWS is exceeded' do
+        before do
+          stub_const("#{described_class}::BUFFER_ROWS", 1)
+        end
+
+        it 'updates and continues' do
+          expect(described_class::MergeRequestDiff).to receive(:transaction).twice
+
+          subject.perform(start_id, stop_id)
+        end
+      end
+
+      context 'when BUFFER_ROWS is not exceeded' do
+        it 'only updates once' do
+          expect(described_class::MergeRequestDiff).to receive(:transaction).once
+
+          subject.perform(start_id, stop_id)
+        end
+      end
+    end
+
+    context 'when the merge request diff update fails' do
+      before do
+        allow(described_class::MergeRequestDiff)
+          .to receive(:update_all).and_raise(ActiveRecord::Rollback)
+      end
+
+      it 'does not add any diff commits' do
+        expect { subject.perform(merge_request_diff.id, merge_request_diff.id) }
+          .not_to change { MergeRequestDiffCommit.count }
+      end
+
+      it 'does not add any diff files' do
+        expect { subject.perform(merge_request_diff.id, merge_request_diff.id) }
+          .not_to change { MergeRequestDiffFile.count }
+      end
+    end
+
+    context 'when the merge request diff has valid commits and diffs' do
+      let(:commits) { merge_request_diff.commits.map(&:to_hash) }
+      let(:diffs) { diffs_to_hashes(merge_request_diff.merge_request_diff_files) }
+      let(:expected_diffs) { diffs }
+
+      include_examples 'updated MR diff'
+    end
+
+    context 'when the merge request diffs have binary content' do
+      let(:commits) { merge_request_diff.commits.map(&:to_hash) }
+      let(:expected_diffs) { diffs }
+
+      # The start of a PDF created by Illustrator
+      let(:binary_string) do
+        "\x25\x50\x44\x46\x2d\x31\x2e\x35\x0d\x25\xe2\xe3\xcf\xd3\x0d\x0a".force_encoding(Encoding::BINARY)
+      end
+
+      let(:diffs) do
+        [
+          {
+            'diff' => binary_string,
+            'new_path' => 'path',
+            'old_path' => 'path',
+            'a_mode' => '100644',
+            'b_mode' => '100644',
+            'new_file' => false,
+            'renamed_file' => false,
+            'deleted_file' => false,
+            'too_large' => false
+          }
+        ]
+      end
+
+      include_examples 'updated MR diff'
+    end
+
+    context 'when the merge request diff has commits, but no diffs' do
+      let(:commits) { merge_request_diff.commits.map(&:to_hash) }
+      let(:diffs) { [] }
+      let(:expected_diffs) { diffs }
+
+      include_examples 'updated MR diff'
+    end
+
+    context 'when the merge request diffs have invalid content' do
+      let(:commits) { merge_request_diff.commits.map(&:to_hash) }
+      let(:diffs) { ['--broken-diff'] }
+      let(:expected_diffs) { [] }
+
+      include_examples 'updated MR diff'
+    end
+
+    context 'when the merge request diffs are Rugged::Patch instances' do
+      let(:commits) { merge_request_diff.commits.map(&:to_hash) }
+      let(:first_commit) { merge_request.project.repository.commit(merge_request_diff.head_commit_sha) }
+      let(:diffs) { first_commit.diff_from_parent.patches }
+      let(:expected_diffs) { [] }
+
+      include_examples 'updated MR diff'
+    end
+
+    context 'when the merge request diffs are Rugged::Diff::Delta instances' do
+      let(:commits) { merge_request_diff.commits.map(&:to_hash) }
+      let(:first_commit) { merge_request.project.repository.commit(merge_request_diff.head_commit_sha) }
+      let(:diffs) { first_commit.diff_from_parent.deltas }
+      let(:expected_diffs) { [] }
+
+      include_examples 'updated MR diff'
+    end
+  end
+end
diff --git a/spec/migrations/schedule_merge_request_diff_migrations_spec.rb b/spec/migrations/schedule_merge_request_diff_migrations_spec.rb
new file mode 100644
index 00000000000..f95bd6e3511
--- /dev/null
+++ b/spec/migrations/schedule_merge_request_diff_migrations_spec.rb
@@ -0,0 +1,59 @@
+require 'spec_helper'
+require Rails.root.join('db', 'post_migrate', '20170703130158_schedule_merge_request_diff_migrations')
+
+describe ScheduleMergeRequestDiffMigrations, :migration, :sidekiq do
+  matcher :be_scheduled_migration do |time, *expected|
+    match do |migration|
+      BackgroundMigrationWorker.jobs.any? do |job|
+        job['args'] == [migration, expected] &&
+          job['at'].to_i == time.to_i
+      end
+    end
+
+    failure_message do |migration|
+      "Migration `#{migration}` with args `#{expected.inspect}` not scheduled!"
+    end
+  end
+
+  let(:merge_request_diffs) { table(:merge_request_diffs) }
+  let(:merge_requests) { table(:merge_requests) }
+  let(:projects) { table(:projects) }
+
+  before do
+    stub_const("#{described_class.name}::BATCH_SIZE", 1)
+
+    projects.create!(id: 1, name: 'gitlab', path: 'gitlab')
+
+    merge_requests.create!(id: 1, target_project_id: 1, source_project_id: 1, target_branch: 'feature', source_branch: 'master')
+
+    merge_request_diffs.create!(id: 1, merge_request_id: 1, st_commits: YAML.dump([]), st_diffs: nil)
+    merge_request_diffs.create!(id: 2, merge_request_id: 1, st_commits: nil, st_diffs: YAML.dump([]))
+    merge_request_diffs.create!(id: 3, merge_request_id: 1, st_commits: nil, st_diffs: nil)
+    merge_request_diffs.create!(id: 4, merge_request_id: 1, st_commits: YAML.dump([]), st_diffs: YAML.dump([]))
+  end
+
+  it 'correctly schedules background migrations' do
+    Sidekiq::Testing.fake! do
+      Timecop.freeze do
+        migrate!
+
+        expect(described_class::MIGRATION).to be_scheduled_migration(5.minutes.from_now, 1, 1)
+        expect(described_class::MIGRATION).to be_scheduled_migration(10.minutes.from_now, 2, 2)
+        expect(described_class::MIGRATION).to be_scheduled_migration(15.minutes.from_now, 4, 4)
+        expect(BackgroundMigrationWorker.jobs.size).to eq 3
+      end
+    end
+  end
+
+  it 'schedules background migrations' do
+    Sidekiq::Testing.inline! do
+      non_empty = 'st_commits IS NOT NULL OR st_diffs IS NOT NULL'
+
+      expect(merge_request_diffs.where(non_empty).count).to eq 3
+
+      migrate!
+
+      expect(merge_request_diffs.where(non_empty).count).to eq 0
+    end
+  end
+end