diff --git a/app/controllers/v3/feature_flags_controller.rb b/app/controllers/v3/feature_flags_controller.rb
index f68067968e2..d74d6db2cf9 100644
--- a/app/controllers/v3/feature_flags_controller.rb
+++ b/app/controllers/v3/feature_flags_controller.rb
@@ -6,6 +6,8 @@
 require 'fetchers/feature_flag_list_fetcher'
 
 class FeatureFlagsController < ApplicationController
+  OVERRIDE_IN_MANIFEST_MSG = 'The feature flag has an override configured in the bosh manifest and can be overwritten when the deployment is updated.'.freeze
+
   def index
     message = FeatureFlagsListMessage.from_params(query_params)
     invalid_param!(message.errors.full_messages) unless message.valid?
@@ -38,6 +40,7 @@ def update
     unprocessable!(message.errors.full_messages) unless message.valid?
 
     flag = VCAP::CloudController::FeatureFlagUpdate.new.update(flag, message)
+    add_warning_headers([OVERRIDE_IN_MANIFEST_MSG]) if VCAP::CloudController::FeatureFlag.config_overridden?(hashed_params[:name].to_sym)
     render status: :ok, json: Presenters::V3::FeatureFlagPresenter.new(flag)
   rescue FeatureFlagUpdate::Error => e
     unprocessable!(e)
diff --git a/app/models/runtime/feature_flag.rb b/app/models/runtime/feature_flag.rb
index 75c452eb6d7..88a5c24a353 100644
--- a/app/models/runtime/feature_flag.rb
+++ b/app/models/runtime/feature_flag.rb
@@ -37,6 +37,8 @@ class UndefinedFeatureFlagError < StandardError
 
     ADMIN_READ_ONLY_SKIPPABLE = [:space_developer_env_var_visibility].freeze
 
+    @feature_flag_overrides = nil
+
     export_attributes :name, :enabled, :error_message
     import_attributes :name, :enabled, :error_message
 
@@ -104,6 +106,12 @@ def self.override_default_flags(feature_flag_overrides)
         feature_flag.enabled = flag_value
         feature_flag.save
       end
+
+      @feature_flag_overrides = feature_flag_overrides
+    end
+
+    def self.config_overridden?(feature_flag_name)
+      @feature_flag_overrides && @feature_flag_overrides.keys.include?(feature_flag_name)
     end
 
     private_class_method :admin?
diff --git a/spec/unit/controllers/v3/feature_flags_controller_spec.rb b/spec/unit/controllers/v3/feature_flags_controller_spec.rb
index 6d59fa1c2de..91b86223c1d 100644
--- a/spec/unit/controllers/v3/feature_flags_controller_spec.rb
+++ b/spec/unit/controllers/v3/feature_flags_controller_spec.rb
@@ -230,6 +230,51 @@
           expect(parsed_body['custom_error_message']).to be_nil
         end
       end
+
+      context 'when there are overrides in configuration' do
+        before do
+          stub_const('VCAP::CloudController::FeatureFlag::DEFAULT_FLAGS', {
+                       flag1: false, flag2: true, flag3: true, flag4: false
+                     })
+          VCAP::CloudController::FeatureFlag.override_default_flags({ flag1: false, flag4: true })
+        end
+
+        it 'returns a warning message for the overridden flags' do
+          patch :update, params: {
+            name: 'flag1',
+            enabled: false
+          }, as: :json
+
+          expect(response).to have_http_status :ok
+          expect(response).to have_warning_message FeatureFlagsController::OVERRIDE_IN_MANIFEST_MSG
+
+          patch :update, params: {
+            name: 'flag4',
+            enabled: false
+          }, as: :json
+
+          expect(response).to have_http_status :ok
+          expect(response).to have_warning_message FeatureFlagsController::OVERRIDE_IN_MANIFEST_MSG
+        end
+
+        it 'returns no warning message for not overridden flags' do
+          patch :update, params: {
+            name: 'flag2',
+            enabled: false
+          }, as: :json
+
+          expect(response).to have_http_status :ok
+          expect(response.headers['X-Cf-Warnings']).to be_nil
+
+          patch :update, params: {
+            name: 'flag3',
+            enabled: false
+          }, as: :json
+
+          expect(response).to have_http_status :ok
+          expect(response.headers['X-Cf-Warnings']).to be_nil
+        end
+      end
     end
   end
 end
diff --git a/spec/unit/models/runtime/feature_flag_spec.rb b/spec/unit/models/runtime/feature_flag_spec.rb
index 82dea09e712..458f93c4cdd 100644
--- a/spec/unit/models/runtime/feature_flag_spec.rb
+++ b/spec/unit/models/runtime/feature_flag_spec.rb
@@ -332,5 +332,33 @@ module VCAP::CloudController
         end
       end
     end
+
+    describe '.config_overridden?' do
+      context 'when overrides have not been set yet' do
+        before do
+          FeatureFlag.instance_variable_set(:@feature_flag_overrides, nil)
+        end
+
+        it 'returns nil' do
+          expect(FeatureFlag.config_overridden?(:diego_docker)).to be_nil
+        end
+      end
+
+      context 'when overrides have been set' do
+        let(:default_diego_docker_value) { FeatureFlag::DEFAULT_FLAGS[:diego_docker] }
+
+        before do
+          FeatureFlag.override_default_flags({ diego_docker: !default_diego_docker_value })
+        end
+
+        it 'return true for the overriden flag' do
+          expect(FeatureFlag.config_overridden?(:diego_docker)).to be true
+        end
+
+        it 'return false for other flags' do
+          expect(FeatureFlag.config_overridden?(:potato)).to be false
+        end
+      end
+    end
   end
 end