diff --git a/app/models/site_statistic.rb b/app/models/site_statistic.rb
index daac1c57db9070d4744cc9d2c1e03cb8b120731f..48324570f0bd138a5beafa5c27ecc4f5e00178a9 100644
--- a/app/models/site_statistic.rb
+++ b/app/models/site_statistic.rb
@@ -49,7 +49,7 @@ def self.with_statistics_available(raw_attribute)
   #
   # @return [SiteStatistic] record with tracked information
   def self.fetch
-    SiteStatistic.transaction(requires_new: true) do
+    transaction(requires_new: true) do
       SiteStatistic.first_or_create!
     end
   rescue ActiveRecord::RecordNotUnique
diff --git a/changelogs/unreleased/repopulate_site_statistics.yml b/changelogs/unreleased/repopulate_site_statistics.yml
new file mode 100644
index 0000000000000000000000000000000000000000..1961088061d8eab00e2a673def0c763e05506f6a
--- /dev/null
+++ b/changelogs/unreleased/repopulate_site_statistics.yml
@@ -0,0 +1,5 @@
+---
+title: Migrate NULL wiki_access_level to correct number so we count active wikis correctly
+merge_request: 21030
+author:
+type: changed
diff --git a/db/post_migrate/20180809195358_migrate_null_wiki_access_levels.rb b/db/post_migrate/20180809195358_migrate_null_wiki_access_levels.rb
new file mode 100644
index 0000000000000000000000000000000000000000..0a0a33299e442bf58283a00d433a7c94d10abb00
--- /dev/null
+++ b/db/post_migrate/20180809195358_migrate_null_wiki_access_levels.rb
@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+class MigrateNullWikiAccessLevels < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+
+  disable_ddl_transaction!
+
+  class ProjectFeature < ActiveRecord::Base
+    include EachBatch
+
+    self.table_name = 'project_features'
+  end
+
+  def up
+    ProjectFeature.where(wiki_access_level: nil).each_batch do |relation|
+      relation.update_all(wiki_access_level: 20)
+    end
+
+    # We need to re-count wikis as previous attempt was not considering the NULLs.
+    transaction do
+      execute('SET LOCAL statement_timeout TO 0') if Gitlab::Database.postgresql? # see https://gitlab.com/gitlab-org/gitlab-ce/issues/48967
+
+      execute("UPDATE site_statistics SET wikis_count = (SELECT COUNT(*) FROM project_features WHERE wiki_access_level != 0)")
+    end
+  end
+
+  def down
+    # there is no way to rollback this change, there are no downsides in keeping migrated data.
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index edc1cfd1a0ffa906a787b497c901cad108771d8e..a74882e19e2dc935efde66148824874380166207 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: 20180808162000) do
+ActiveRecord::Schema.define(version: 20180809195358) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
diff --git a/lib/tasks/gitlab/site_statistics.rake b/lib/tasks/gitlab/site_statistics.rake
new file mode 100644
index 0000000000000000000000000000000000000000..7d24ec72a9d4159026cd3a44643e466a62295f34
--- /dev/null
+++ b/lib/tasks/gitlab/site_statistics.rake
@@ -0,0 +1,23 @@
+namespace :gitlab do
+  desc "GitLab | Refresh Site Statistics counters"
+  task refresh_site_statistics: :environment do
+    puts 'Updating Site Statistics counters: '
+
+    print '* Repositories... '
+    SiteStatistic.transaction do
+      # see https://gitlab.com/gitlab-org/gitlab-ce/issues/48967
+      ActiveRecord::Base.connection.execute('SET LOCAL statement_timeout TO 0') if Gitlab::Database.postgresql?
+      SiteStatistic.update_all('repositories_count = (SELECT COUNT(*) FROM projects)')
+    end
+    puts 'OK!'.color(:green)
+
+    print '* Wikis... '
+    SiteStatistic.transaction do
+      # see https://gitlab.com/gitlab-org/gitlab-ce/issues/48967
+      ActiveRecord::Base.connection.execute('SET LOCAL statement_timeout TO 0') if Gitlab::Database.postgresql?
+      SiteStatistic.update_all('wikis_count = (SELECT COUNT(*) FROM project_features WHERE wiki_access_level != 0)')
+    end
+    puts 'OK!'.color(:green)
+    puts
+  end
+end
diff --git a/spec/lib/gitlab/bare_repository_import/importer_spec.rb b/spec/lib/gitlab/bare_repository_import/importer_spec.rb
index 6e21c846c0ad60451db0f7fe9210274f1af06f62..3c63e601abc366c5abc20fa32be1d8a59eb444f9 100644
--- a/spec/lib/gitlab/bare_repository_import/importer_spec.rb
+++ b/spec/lib/gitlab/bare_repository_import/importer_spec.rb
@@ -10,9 +10,6 @@
   subject(:importer) { described_class.new(admin, bare_repository) }
 
   before do
-    @rainbow = Rainbow.enabled
-    Rainbow.enabled = false
-
     allow(described_class).to receive(:log)
   end
 
@@ -20,7 +17,6 @@
     FileUtils.rm_rf(base_dir)
     TestEnv.clean_test_path
     ensure_seeds
-    Rainbow.enabled = @rainbow
   end
 
   shared_examples 'importing a repository' do
diff --git a/spec/lib/system_check/simple_executor_spec.rb b/spec/lib/system_check/simple_executor_spec.rb
index 9da3648400e00797c7ee8d6c7670df47b58d3047..e71e9da369d9d73e6bc9df16f0a4effa4fd78ac7 100644
--- a/spec/lib/system_check/simple_executor_spec.rb
+++ b/spec/lib/system_check/simple_executor_spec.rb
@@ -98,15 +98,6 @@ def check?
     end
   end
 
-  before do
-    @rainbow = Rainbow.enabled
-    Rainbow.enabled = false
-  end
-
-  after do
-    Rainbow.enabled = @rainbow
-  end
-
   describe '#component' do
     it 'returns stored component name' do
       expect(subject.component).to eq('Test')
diff --git a/spec/migrations/migrate_null_wiki_access_levels_spec.rb b/spec/migrations/migrate_null_wiki_access_levels_spec.rb
new file mode 100644
index 0000000000000000000000000000000000000000..f99273072a2f03a9ff7857813c87f428a3436569
--- /dev/null
+++ b/spec/migrations/migrate_null_wiki_access_levels_spec.rb
@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+require Rails.root.join('db', 'post_migrate', '20180809195358_migrate_null_wiki_access_levels.rb')
+
+describe MigrateNullWikiAccessLevels, :migration do
+  let(:namespaces) { table('namespaces') }
+  let(:projects) { table(:projects) }
+  let(:project_features) { table(:project_features) }
+  let(:migration) { described_class.new }
+
+  before do
+    namespace = namespaces.create(name: 'foo', path: 'foo')
+
+    projects.create!(id: 1, name: 'gitlab1', path: 'gitlab1', namespace_id: namespace.id)
+    projects.create!(id: 2, name: 'gitlab2', path: 'gitlab2', namespace_id: namespace.id)
+    projects.create!(id: 3, name: 'gitlab3', path: 'gitlab3', namespace_id: namespace.id)
+
+    project_features.create!(id: 1, project_id: 1, wiki_access_level: nil)
+    project_features.create!(id: 2, project_id: 2, wiki_access_level: 10)
+    project_features.create!(id: 3, project_id: 3, wiki_access_level: 20)
+  end
+
+  describe '#up' do
+    it 'migrates existing project_features with wiki_access_level NULL to 20' do
+      expect { migration.up }.to change { project_features.where(wiki_access_level: 20).count }.by(1)
+    end
+  end
+end
diff --git a/spec/spec_helper.rb b/spec/spec_helper.rb
index fb250526bcacb5bd86a2d15f83811536a8d6b626..198499237594ff88f2cef57fc0289f5ab69e7252 100644
--- a/spec/spec_helper.rb
+++ b/spec/spec_helper.rb
@@ -29,6 +29,7 @@
 
 # require rainbow gem String monkeypatch, so we can test SystemChecks
 require 'rainbow/ext/string'
+Rainbow.enabled = false
 
 require_relative '../ee/spec/spec_helper'
 
diff --git a/spec/tasks/gitlab/site_statistics_rake_spec.rb b/spec/tasks/gitlab/site_statistics_rake_spec.rb
new file mode 100644
index 0000000000000000000000000000000000000000..20f0df65e63f66ba23d1c41f34798396c4fdb272
--- /dev/null
+++ b/spec/tasks/gitlab/site_statistics_rake_spec.rb
@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+require 'rake_helper'
+
+describe 'rake gitlab:refresh_site_statistics' do
+  before do
+    Rake.application.rake_require 'tasks/gitlab/site_statistics'
+
+    create(:project)
+    SiteStatistic.fetch.update(repositories_count: 0, wikis_count: 0)
+  end
+
+  let(:task) { 'gitlab:refresh_site_statistics' }
+
+  it 'recalculates existing counters' do
+    run_rake_task(task)
+
+    expect(SiteStatistic.fetch.repositories_count).to eq(1)
+    expect(SiteStatistic.fetch.wikis_count).to eq(1)
+  end
+
+  it 'displays message listing counters' do
+    expect { run_rake_task(task) }.to output(/Updating Site Statistics counters:.* Repositories\.\.\. OK!.* Wikis\.\.\. OK!/m).to_stdout
+  end
+end