diff --git a/packages/compass-aggregations/README.md b/packages/compass-aggregations/README.md
index 4425d97c165..9d5a92c689b 100644
--- a/packages/compass-aggregations/README.md
+++ b/packages/compass-aggregations/README.md
@@ -94,7 +94,6 @@ const aggregationsStore = configureAggregationsStore({
   namespace: 'db.coll',
   serverVersion: '4.2.0',
   fields: [],
-  isAtlasDeployed: true,
   outResultsFn: handleOut,
   env: 'atlas',
   localAppRegistry: appRegistry
diff --git a/packages/compass-aggregations/src/components/aggregations/aggregations.jsx b/packages/compass-aggregations/src/components/aggregations/aggregations.jsx
index 29f34d817c8..b38a56a6ce8 100644
--- a/packages/compass-aggregations/src/components/aggregations/aggregations.jsx
+++ b/packages/compass-aggregations/src/components/aggregations/aggregations.jsx
@@ -52,7 +52,6 @@ const mapStateToProps = (state) => ({
   name: state.name,
   collationString: state.collationString,
   isCommenting: state.comments,
-  isAtlasDeployed: state.isAtlasDeployed,
   isAutoPreviewing: state.autoPreview,
   settings: state.settings,
   limit: state.limit,
diff --git a/packages/compass-aggregations/src/components/pipeline-builder-workspace/pipeline-as-text-workspace/pipeline-stages-preview.spec.tsx b/packages/compass-aggregations/src/components/pipeline-builder-workspace/pipeline-as-text-workspace/pipeline-stages-preview.spec.tsx
index b9fc883cbf6..f9d483311f1 100644
--- a/packages/compass-aggregations/src/components/pipeline-builder-workspace/pipeline-as-text-workspace/pipeline-stages-preview.spec.tsx
+++ b/packages/compass-aggregations/src/components/pipeline-builder-workspace/pipeline-as-text-workspace/pipeline-stages-preview.spec.tsx
@@ -9,6 +9,7 @@ import userEvent from '@testing-library/user-event';
 import configureStore from '../../../../test/configure-store';
 
 import { OutputStagePreview } from './pipeline-stages-preview';
+import preferencesAccess from 'compass-preferences-model';
 
 const renderStageBanner = (
   props: Partial<ComponentProps<typeof OutputStagePreview>> = {}
@@ -17,7 +18,6 @@ const renderStageBanner = (
     <Provider store={configureStore()}>
       <OutputStagePreview
         stageOperator="$out"
-        isAtlas={false}
         isComplete={false}
         isLoading={false}
         onOpenCollection={() => {}}
@@ -30,12 +30,9 @@ const renderStageBanner = (
 
 describe('OutputStagePreview', function () {
   (['$out', '$merge'] as const).forEach((stageOperator) => {
-    describe(`${stageOperator} - not on atlas`, function () {
+    describe(`${stageOperator} with run aggregation enabled`, function () {
       it('renders stage banner', function () {
-        renderStageBanner({
-          stageOperator,
-          isAtlas: false,
-        });
+        renderStageBanner({ stageOperator });
         expect(screen.getByTestId(`${stageOperator}-preview-banner`)).to.exist;
         expect(() => {
           screen.getByRole('button', {
@@ -45,11 +42,28 @@ describe('OutputStagePreview', function () {
       });
     });
 
-    describe(`${stageOperator} on atlas`, function () {
+    describe(`${stageOperator} with run aggregation disabled`, function () {
+      let enableAggregationBuilderRunPipeline: boolean;
+
+      before(async function () {
+        enableAggregationBuilderRunPipeline =
+          preferencesAccess.getPreferences()
+            .enableAggregationBuilderRunPipeline;
+
+        await preferencesAccess.savePreferences({
+          enableAggregationBuilderRunPipeline: false,
+        });
+      });
+
+      after(async function () {
+        await preferencesAccess.savePreferences({
+          enableAggregationBuilderRunPipeline,
+        });
+      });
+
       it(`renders stage banner`, function () {
         renderStageBanner({
           stageOperator,
-          isAtlas: true,
         });
         expect(screen.getByTestId(`${stageOperator}-preview-banner`)).to.exist;
       });
@@ -57,7 +71,6 @@ describe('OutputStagePreview', function () {
       it(`renders stage action`, function () {
         renderStageBanner({
           stageOperator,
-          isAtlas: true,
         });
         expect(
           screen.getByRole('button', {
@@ -70,7 +83,6 @@ describe('OutputStagePreview', function () {
         const onSaveCollection = sinon.spy();
         renderStageBanner({
           stageOperator,
-          isAtlas: true,
           onSaveCollection,
         });
         const button = screen.getByRole('button', {
@@ -84,7 +96,6 @@ describe('OutputStagePreview', function () {
       it('renders loading state', function () {
         renderStageBanner({
           stageOperator,
-          isAtlas: true,
           isLoading: true,
         });
         const button = screen.getByRole('button', {
@@ -96,7 +107,6 @@ describe('OutputStagePreview', function () {
       it('renders complete state', function () {
         renderStageBanner({
           stageOperator,
-          isAtlas: true,
           isComplete: true,
         });
         expect(screen.getByTestId(`${stageOperator}-is-complete-banner`)).to
@@ -106,7 +116,6 @@ describe('OutputStagePreview', function () {
       it('renders complete state action button', function () {
         renderStageBanner({
           stageOperator,
-          isAtlas: true,
           isComplete: true,
         });
         const button = screen.getByRole('button', {
@@ -119,7 +128,6 @@ describe('OutputStagePreview', function () {
         const onOpenCollection = sinon.spy();
         renderStageBanner({
           stageOperator,
-          isAtlas: true,
           isComplete: true,
           onOpenCollection,
         });
diff --git a/packages/compass-aggregations/src/components/pipeline-builder-workspace/pipeline-as-text-workspace/pipeline-stages-preview.tsx b/packages/compass-aggregations/src/components/pipeline-builder-workspace/pipeline-as-text-workspace/pipeline-stages-preview.tsx
index 8878e17e137..1c6cdec0e61 100644
--- a/packages/compass-aggregations/src/components/pipeline-builder-workspace/pipeline-as-text-workspace/pipeline-stages-preview.tsx
+++ b/packages/compass-aggregations/src/components/pipeline-builder-workspace/pipeline-as-text-workspace/pipeline-stages-preview.tsx
@@ -20,6 +20,7 @@ import {
   MERGE_STAGE_PREVIEW_TEXT,
   OUT_STAGE_PREVIEW_TEXT,
 } from '../../../constants';
+import { usePreference } from 'compass-preferences-model';
 
 const bannerStyles = css({
   alignItems: 'center',
@@ -39,7 +40,6 @@ const actionButtonStyles = css({
 
 type OutputStageProps = {
   stageOperator: '$out' | '$merge' | null;
-  isAtlas: boolean;
   isLoading: boolean;
   isComplete: boolean;
   onSaveCollection: () => void;
@@ -77,16 +77,23 @@ const PipelineStageBanner = ({
 
 export const OutputStagePreview = ({
   stageOperator,
-  isAtlas,
   isLoading,
   isComplete,
   onSaveCollection,
   onOpenCollection,
 }: OutputStageProps) => {
+  // When explicit pipeline run is not enabled, we allow to run output stage
+  // from the preview
+  const showOutputActions = !usePreference(
+    'enableAggregationBuilderRunPipeline',
+    React
+  );
+
   if (!stageOperator) {
     return null;
   }
-  if (isComplete && isAtlas) {
+
+  if (isComplete && showOutputActions) {
     return (
       <PipelineStageBanner
         data-testid={`${stageOperator}-is-complete-banner`}
@@ -110,7 +117,7 @@ export const OutputStagePreview = ({
           : MERGE_STAGE_PREVIEW_TEXT
       }
       actionButton={
-        isAtlas ? (
+        showOutputActions ? (
           <Button
             {...buttonProps}
             disabled={isLoading}
@@ -126,7 +133,6 @@ export const OutputStagePreview = ({
 };
 
 const mapState = ({
-  isAtlasDeployed,
   pipelineBuilder: {
     textEditor: {
       outputStage: { isComplete, isLoading },
@@ -134,7 +140,6 @@ const mapState = ({
   },
 }: RootState) => {
   return {
-    isAtlas: isAtlasDeployed,
     isComplete,
     isLoading,
   };
diff --git a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/index.tsx b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/index.tsx
index 0ee2a8f8e0a..bbb0aa3c074 100644
--- a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/index.tsx
+++ b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/index.tsx
@@ -147,6 +147,6 @@ export const PipelineHeader: React.FunctionComponent<PipelineHeaderProps> = ({
 
 export default connect((state: RootState) => {
   return {
-    isOpenPipelineVisible: !state.editViewName && !state.isAtlasDeployed,
+    isOpenPipelineVisible: !state.editViewName,
   };
 })(PipelineHeader);
diff --git a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/pipeline-actions.spec.tsx b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/pipeline-actions.spec.tsx
index 53b51c1a1ed..0d53a3d8b15 100644
--- a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/pipeline-actions.spec.tsx
+++ b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/pipeline-actions.spec.tsx
@@ -8,6 +8,7 @@ import ConnectedPipelineActions, { PipelineActions } from './pipeline-actions';
 import configureStore from '../../../../test/configure-store';
 import { Provider } from 'react-redux';
 import { changeStageDisabled } from '../../../modules/pipeline-builder/stage-editor';
+import preferencesAccess from 'compass-preferences-model';
 
 describe('PipelineActions', function () {
   afterEach(cleanup);
@@ -104,7 +105,6 @@ describe('PipelineActions', function () {
           onExportAggregationResults={() => {}}
           onUpdateView={() => {}}
           onExplainAggregation={() => {}}
-          isAtlasDeployed={false}
           onCollectionScanInsightActionButtonClick={() => {}}
           onShowAIInputClick={() => {}}
         />
@@ -125,9 +125,25 @@ describe('PipelineActions', function () {
     });
   });
 
-  describe('options disabled in atlas', function () {
+  describe('extra options disabled', function () {
+    let enableAggregationBuilderExtraOptions: boolean;
     let onRunAggregationSpy: SinonSpy;
     let onToggleOptionsSpy: SinonSpy;
+
+    before(async function () {
+      enableAggregationBuilderExtraOptions =
+        preferencesAccess.getPreferences().enableAggregationBuilderExtraOptions;
+      await preferencesAccess.savePreferences({
+        enableAggregationBuilderExtraOptions: false,
+      });
+    });
+
+    after(async function () {
+      await preferencesAccess.savePreferences({
+        enableAggregationBuilderExtraOptions,
+      });
+    });
+
     beforeEach(function () {
       onRunAggregationSpy = spy();
       onToggleOptionsSpy = spy();
@@ -143,7 +159,6 @@ describe('PipelineActions', function () {
           onExportAggregationResults={() => {}}
           onUpdateView={() => {}}
           onExplainAggregation={() => {}}
-          isAtlasDeployed={true}
           onCollectionScanInsightActionButtonClick={() => {}}
           onShowAIInputClick={() => {}}
         />
diff --git a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/pipeline-actions.tsx b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/pipeline-actions.tsx
index 0696b0058aa..beb20d4fb5c 100644
--- a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/pipeline-actions.tsx
+++ b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-header/pipeline-actions.tsx
@@ -54,8 +54,6 @@ type PipelineActionsProps = {
   isOptionsVisible?: boolean;
   onToggleOptions: () => void;
 
-  isAtlasDeployed?: boolean;
-
   showAIEntry: boolean;
   onShowAIInputClick: () => void;
 
@@ -80,10 +78,13 @@ export const PipelineActions: React.FunctionComponent<PipelineActionsProps> = ({
   onToggleOptions,
   onExportAggregationResults,
   onExplainAggregation,
-  isAtlasDeployed,
   showCollectionScanInsight,
   onCollectionScanInsightActionButtonClick,
 }) => {
+  const enableAggregationBuilderExtraOptions = usePreference(
+    'enableAggregationBuilderExtraOptions',
+    React
+  );
   const showInsights = usePreference('showInsights', React);
   const isAIFeatureEnabled = useIsAIFeatureEnabled(React);
 
@@ -151,7 +152,7 @@ export const PipelineActions: React.FunctionComponent<PipelineActionsProps> = ({
           Run
         </Button>
       )}
-      {!isAtlasDeployed && (
+      {enableAggregationBuilderExtraOptions && (
         <MoreOptionsToggle
           isExpanded={!!isOptionsVisible}
           aria-controls="pipeline-options"
@@ -181,7 +182,6 @@ const mapState = (state: RootState) => {
       isBuilderView,
     showUpdateViewButton: Boolean(state.editViewName),
     isUpdateViewButtonDisabled: !state.isModified || hasSyntaxErrors,
-    isAtlasDeployed: state.isAtlasDeployed,
     showCollectionScanInsight: state.insights.isCollectionScan,
   };
 };
diff --git a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-settings/index.spec.tsx b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-settings/index.spec.tsx
index 369d4a6302c..241b43e87eb 100644
--- a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-settings/index.spec.tsx
+++ b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-settings/index.spec.tsx
@@ -20,7 +20,6 @@ describe('PipelineSettings', function () {
       <Provider store={configureStore()}>
         <PipelineSettings
           isExportToLanguageEnabled={true}
-          isCreatePipelineDisplayed={true}
           onExportToLanguage={onExportToLanguageSpy}
           onCreateNewPipeline={onCreateNewPipelineSpy}
         />
diff --git a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-settings/index.tsx b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-settings/index.tsx
index a69b15852cf..49696b968fa 100644
--- a/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-settings/index.tsx
+++ b/packages/compass-aggregations/src/components/pipeline-toolbar/pipeline-settings/index.tsx
@@ -8,6 +8,7 @@ import PipelineExtraSettings from './pipeline-extra-settings';
 import type { RootState } from '../../../modules';
 import { getIsPipelineInvalidFromBuilderState } from '../../../modules/pipeline-builder/builder-helpers';
 import { confirmNewPipeline } from '../../../modules/is-new-pipeline-confirm';
+import { usePreference } from 'compass-preferences-model';
 
 const containerStyles = css({
   display: 'grid',
@@ -30,8 +31,7 @@ const extraSettingsStyles = css({
 });
 
 type PipelineSettingsProps = {
-  isSavePipelineDisplayed?: boolean;
-  isCreatePipelineDisplayed?: boolean;
+  isEditingViewPipeline?: boolean;
   isExportToLanguageEnabled?: boolean;
   onExportToLanguage: () => void;
   onCreateNewPipeline: () => void;
@@ -40,12 +40,19 @@ type PipelineSettingsProps = {
 export const PipelineSettings: React.FunctionComponent<
   PipelineSettingsProps
 > = ({
-  isSavePipelineDisplayed,
-  isCreatePipelineDisplayed,
+  isEditingViewPipeline = false,
   isExportToLanguageEnabled,
   onExportToLanguage,
   onCreateNewPipeline,
 }) => {
+  const enableSavedAggregationsQueries = usePreference(
+    'enableSavedAggregationsQueries',
+    React
+  );
+  const isSavePipelineDisplayed =
+    !isEditingViewPipeline && enableSavedAggregationsQueries;
+  const isCreatePipelineDisplayed = !isEditingViewPipeline;
+
   return (
     <div className={containerStyles} data-testid="pipeline-settings">
       <div className={settingsStyles}>
@@ -88,8 +95,7 @@ export default connect(
   (state: RootState) => {
     const hasSyntaxErrors = getIsPipelineInvalidFromBuilderState(state, false);
     return {
-      isSavePipelineDisplayed: !state.editViewName && !state.isAtlasDeployed,
-      isCreatePipelineDisplayed: !state.editViewName,
+      isEditingViewPipeline: state.editViewName,
       isExportToLanguageEnabled: !hasSyntaxErrors,
     };
   },
diff --git a/packages/compass-aggregations/src/components/pipeline/pipeline.jsx b/packages/compass-aggregations/src/components/pipeline/pipeline.jsx
index 442ae14e4d8..dababf4cbc1 100644
--- a/packages/compass-aggregations/src/components/pipeline/pipeline.jsx
+++ b/packages/compass-aggregations/src/components/pipeline/pipeline.jsx
@@ -23,7 +23,6 @@ class Pipeline extends PureComponent {
   static displayName = 'PipelineComponent';
 
   static propTypes = {
-    isAtlasDeployed: PropTypes.bool.isRequired,
     saveCurrentPipeline: PropTypes.func.isRequired,
     clonePipeline: PropTypes.func.isRequired,
     isCommenting: PropTypes.bool.isRequired,
@@ -115,7 +114,6 @@ class Pipeline extends PureComponent {
     return (
       <div className={styles.pipeline}>
         <Settings
-          isAtlasDeployed={this.props.isAtlasDeployed}
           isExpanded={this.props.settings.isExpanded}
           toggleSettingsIsExpanded={this.props.toggleSettingsIsExpanded}
           toggleSettingsIsCommentMode={this.props.toggleSettingsIsCommentMode}
diff --git a/packages/compass-aggregations/src/components/settings/settings.spec.jsx b/packages/compass-aggregations/src/components/settings/settings.spec.jsx
index 7fc49c76051..4858f2ee3db 100644
--- a/packages/compass-aggregations/src/components/settings/settings.spec.jsx
+++ b/packages/compass-aggregations/src/components/settings/settings.spec.jsx
@@ -28,7 +28,6 @@ describe('Settings [Component]', function () {
       state = {
         ...INITIAL_STATE,
         applySettings: applySettingsSpy,
-        isAtlasDeployed: false,
         toggleSettingsIsExpanded: toggleSettingsIsExpandedSpy,
         toggleSettingsIsCommentMode: toggleSettingsIsCommentModeSpy,
         setSettingsSampleSize: setSettingsSampleSizeSpy,
@@ -125,7 +124,7 @@ describe('Settings [Component]', function () {
     });
 
     it('hides the large limit option', function () {
-      const props = { ...state, isAtlasDeployed: true };
+      const props = { ...state };
       component = mount(<Settings {...props} />);
       expect(component.find('label[innerText="Limit"]')).to.not.be.present();
     });
diff --git a/packages/compass-aggregations/src/components/settings/settings.tsx b/packages/compass-aggregations/src/components/settings/settings.tsx
index 23efac04e67..9822fcc3865 100644
--- a/packages/compass-aggregations/src/components/settings/settings.tsx
+++ b/packages/compass-aggregations/src/components/settings/settings.tsx
@@ -14,6 +14,7 @@ import {
 } from '@mongodb-js/compass-components';
 
 import { DEFAULT_SAMPLE_SIZE, DEFAULT_LARGE_LIMIT } from '../../constants';
+import { usePreference } from 'compass-preferences-model';
 
 const aggregationCommentModeId = 'aggregation-comment-mode';
 const aggregationCommentModeDescriptionId =
@@ -90,7 +91,6 @@ const inputControlStyles = css({
 const inputMetaStyles = css({ flexGrow: 1, p: { marginTop: spacing[2] } });
 
 type SettingsProps = {
-  isAtlasDeployed: boolean;
   isCommenting: boolean;
   isExpanded: boolean;
   largeLimit: number;
@@ -110,7 +110,6 @@ type SettingsProps = {
 };
 
 function Settings({
-  isAtlasDeployed,
   isCommenting,
   isExpanded,
   largeLimit,
@@ -122,6 +121,10 @@ function Settings({
   toggleSettingsIsCommentMode,
   toggleSettingsIsExpanded,
 }: SettingsProps) {
+  const enableAggregationBuilderExtraOptions = usePreference(
+    'enableAggregationBuilderExtraOptions',
+    React
+  );
   const darkMode = useDarkMode();
   const onSampleSizeChanged = useCallback(
     (evt: React.ChangeEvent<HTMLInputElement>) => {
@@ -233,7 +236,7 @@ function Settings({
           />
         </div>
       </div>
-      {!isAtlasDeployed && (
+      {enableAggregationBuilderExtraOptions && (
         <div className={cx(inputGroupStyles, darkMode && inputGroupDarkStyles)}>
           <div className={inputMetaStyles}>
             <Label htmlFor={aggregationLimitId} id={aggregationLimitLabelId}>
diff --git a/packages/compass-aggregations/src/components/stage-preview/output-stage-preview.spec.tsx b/packages/compass-aggregations/src/components/stage-preview/output-stage-preview.spec.tsx
index 3a0cf674e92..3f931ef8542 100644
--- a/packages/compass-aggregations/src/components/stage-preview/output-stage-preview.spec.tsx
+++ b/packages/compass-aggregations/src/components/stage-preview/output-stage-preview.spec.tsx
@@ -22,7 +22,6 @@ const renderOutputStage = (
         isFinishedPersistingDocuments={false}
         destinationNamespace=""
         hasServerError={false}
-        isAtlasDeployed={false}
         onGoToOutputResults={() => {}}
         onRunOutputStage={() => {}}
         {...props}
@@ -95,7 +94,7 @@ describe('OutputStagePreview', function () {
           expect(screen.getByTestId('output-stage-text')).to.exist;
         });
         it('renders save documents button on atlas', function () {
-          renderOutputStage({ operator, isAtlasDeployed: true });
+          renderOutputStage({ operator });
           expect(screen.getByTestId('save-output-documents')).to.exist;
         });
       });
diff --git a/packages/compass-aggregations/src/components/stage-preview/output-stage-preview.tsx b/packages/compass-aggregations/src/components/stage-preview/output-stage-preview.tsx
index 5029b6ed48c..a5d4614b1ee 100644
--- a/packages/compass-aggregations/src/components/stage-preview/output-stage-preview.tsx
+++ b/packages/compass-aggregations/src/components/stage-preview/output-stage-preview.tsx
@@ -20,7 +20,7 @@ import {
   MERGE_STAGE_PREVIEW_TEXT,
   OUT_STAGE_PREVIEW_TEXT,
 } from '../../constants';
-import { parseShellBSON } from '../../modules/pipeline-builder/pipeline-parser/utils';
+import { usePreference } from 'compass-preferences-model';
 
 const stagePreviewStyles = css({
   display: 'flex',
@@ -52,8 +52,7 @@ type OutputStageProps = {
   isLoading: boolean;
   hasServerError: boolean;
   isFinishedPersistingDocuments: boolean;
-  isAtlasDeployed: boolean;
-  destinationNamespace: string;
+  destinationNamespace: string | null;
   onRunOutputStage: () => void;
   onGoToOutputResults: () => void;
 };
@@ -86,11 +85,15 @@ export const OutputStage = ({
   isLoading,
   hasServerError,
   isFinishedPersistingDocuments,
-  isAtlasDeployed,
   destinationNamespace,
   onRunOutputStage,
   onGoToOutputResults,
 }: OutputStageProps) => {
+  const enableAggregationBuilderRunPipeline = usePreference(
+    'enableAggregationBuilderRunPipeline',
+    React
+  );
+
   if (!isOutputStage(operator ?? '')) {
     return null;
   }
@@ -129,7 +132,7 @@ export const OutputStage = ({
           ? MERGE_STAGE_PREVIEW_TEXT
           : OUT_STAGE_PREVIEW_TEXT}
       </div>
-      {isAtlasDeployed && (
+      {enableAggregationBuilderRunPipeline && (
         <Button
           variant="primary"
           data-testid="save-output-documents"
@@ -150,18 +153,16 @@ const mapState = (state: RootState, ownProps: OwnProps) => {
   const stage = state.pipelineBuilder.stageEditor.stages[
     ownProps.index
   ] as StoreStage;
-  const destinationNamespace = getDestinationNamespaceFromStage(
-    state.namespace,
-    parseShellBSON(`{
-      ${stage.stageOperator as string}: ${stage.value ?? ''}
-    }`)
-  );
+  const destinationNamespace = stage.stageOperator
+    ? getDestinationNamespaceFromStage(state.namespace, {
+        [stage.stageOperator]: stage.value ?? '',
+      })
+    : null;
 
   return {
     isLoading: stage.loading,
     hasServerError: !!stage.serverError,
     isFinishedPersistingDocuments: Boolean(stage.previewDocs),
-    isAtlasDeployed: state.isAtlasDeployed,
     destinationNamespace,
     operator: stage.stageOperator,
   };
diff --git a/packages/compass-aggregations/src/modules/index.ts b/packages/compass-aggregations/src/modules/index.ts
index 7bbf4ac37a0..cbf05f9ad11 100644
--- a/packages/compass-aggregations/src/modules/index.ts
+++ b/packages/compass-aggregations/src/modules/index.ts
@@ -15,7 +15,6 @@ import isModified from './is-modified';
 import name from './name';
 import limit from './limit';
 import largeLimit from './large-limit';
-import isAtlasDeployed from './is-atlas-deployed';
 import maxTimeMS from './max-time-ms';
 import collationString from './collation-string';
 import comments from './comments';
@@ -64,7 +63,6 @@ const rootReducer = combineReducers({
   collationString,
   id,
   isModified,
-  isAtlasDeployed,
   settings,
   limit,
   largeLimit,
diff --git a/packages/compass-aggregations/src/modules/is-atlas-deployed.js b/packages/compass-aggregations/src/modules/is-atlas-deployed.js
deleted file mode 100644
index 5b47e49f142..00000000000
--- a/packages/compass-aggregations/src/modules/is-atlas-deployed.js
+++ /dev/null
@@ -1,16 +0,0 @@
-/**
- * The initial state.
- */
-export const INITIAL_STATE = false;
-
-/**
- * The reducer.
- *
- * @param {Boolean} state - The state.
- * @param {Object} action - The action.
- *
- * @returns {Boolean} The state.
- */
-export default function reducer(state = INITIAL_STATE) {
-  return state;
-}
diff --git a/packages/compass-aggregations/src/modules/pipeline-builder/text-editor-output-stage.ts b/packages/compass-aggregations/src/modules/pipeline-builder/text-editor-output-stage.ts
index d6a4a8de4db..d0a411861cc 100644
--- a/packages/compass-aggregations/src/modules/pipeline-builder/text-editor-output-stage.ts
+++ b/packages/compass-aggregations/src/modules/pipeline-builder/text-editor-output-stage.ts
@@ -17,6 +17,7 @@ import type {
   LoadGeneratedPipelineAction,
   PipelineGeneratedFromQueryAction,
 } from './pipeline-ai';
+import preferencesAccess from 'compass-preferences-model';
 
 const enum OutputStageActionTypes {
   FetchStarted = 'compass-aggregations/pipeline-builder/text-editor-output-stage/FetchStarted',
@@ -121,14 +122,18 @@ export const runPipelineWithOutputStage = (): PipelineBuilderThunkAction<
   return async (dispatch, getState, { pipelineBuilder }) => {
     const {
       autoPreview,
-      isAtlasDeployed,
       dataService: { dataService },
       namespace,
       maxTimeMS,
       collationString,
     } = getState();
 
-    if (!dataService || !isAtlasDeployed) {
+    if (
+      !dataService ||
+      // Running output stage from preview is not allowed if "run pipeline"
+      // feature is enabled
+      preferencesAccess.getPreferences().enableAggregationBuilderRunPipeline
+    ) {
       return;
     }
 
diff --git a/packages/compass-aggregations/src/stores/store.spec.ts b/packages/compass-aggregations/src/stores/store.spec.ts
index 992dabed4b9..b19fac1438d 100644
--- a/packages/compass-aggregations/src/stores/store.spec.ts
+++ b/packages/compass-aggregations/src/stores/store.spec.ts
@@ -117,7 +117,6 @@ describe('Aggregation Store', function () {
             },
             serverVersion: INITIAL_STATE.serverVersion,
             isModified: INITIAL_STATE.isModified,
-            isAtlasDeployed: INITIAL_STATE.isAtlasDeployed,
             insights: {
               isCollectionScan: false,
             },
diff --git a/packages/compass-aggregations/src/stores/store.ts b/packages/compass-aggregations/src/stores/store.ts
index cb59538b327..626c8f30e9a 100644
--- a/packages/compass-aggregations/src/stores/store.ts
+++ b/packages/compass-aggregations/src/stores/store.ts
@@ -81,10 +81,6 @@ export type ConfigureStoreOptions = {
    * "atlas" | "on-prem" | "adl"
    */
   env: typeof ENVS[number] | null;
-  /**
-   * Indicates that the plugin is used in Atlas Cloud
-   */
-  isAtlasDeployed: boolean | null;
   /**
    * Namespace field values that will be used in autocomplete
    */
@@ -216,11 +212,6 @@ const configureStore = (options: ConfigureStoreOptions) => {
             | Store
             | undefined
         )?.getState().instance.env,
-      // options.isAtlasDeployed is only used by mms to change some behaviour in the
-      // aggregations plugin
-      isAtlasDeployed:
-        options.isAtlasDeployed !== null &&
-        options.isAtlasDeployed !== undefined,
       // options.fields is only used by mms, but always set to [] which is the initial value anyway
       fields: options.fields ?? [],
       // options.outResultsFn is only used by mms
diff --git a/packages/compass-preferences-model/src/preferences.ts b/packages/compass-preferences-model/src/preferences.ts
index bc169c3ad0a..1eea8cc0b03 100644
--- a/packages/compass-preferences-model/src/preferences.ts
+++ b/packages/compass-preferences-model/src/preferences.ts
@@ -58,6 +58,8 @@ export type UserConfigurablePreferences = PermanentFeatureFlags &
     enableExplainPlan: boolean;
     enableImportExport: boolean;
     enableAggregationBuilderRunPipeline: boolean;
+    enableAggregationBuilderExtraOptions: boolean;
+    enableSavedAggregationsQueries: boolean;
   };
 
 export type InternalUserPreferences = {
@@ -695,6 +697,29 @@ export const storedUserPreferencesProps: Required<{
     type: 'boolean',
   },
 
+  enableAggregationBuilderExtraOptions: {
+    ui: true,
+    cli: true,
+    global: true,
+    description: {
+      short:
+        'Enable preview input limit and collation options in aggregation view',
+    },
+    validator: z.boolean().default(true),
+    type: 'boolean',
+  },
+
+  enableSavedAggregationsQueries: {
+    ui: true,
+    cli: true,
+    global: true,
+    description: {
+      short: 'Enable saving and opening saved aggregations and queries',
+    },
+    validator: z.boolean().default(true),
+    type: 'boolean',
+  },
+
   ...allFeatureFlagsProps,
 };
 
diff --git a/packages/compass-query-bar/src/components/query-bar.spec.tsx b/packages/compass-query-bar/src/components/query-bar.spec.tsx
index 3d15a29076c..b0628436f97 100644
--- a/packages/compass-query-bar/src/components/query-bar.spec.tsx
+++ b/packages/compass-query-bar/src/components/query-bar.spec.tsx
@@ -37,7 +37,6 @@ const renderQueryBar = (
         onApply={noop}
         onReset={noop}
         showExportToLanguageButton
-        showQueryHistoryButton
         resultId="123"
         {...props}
       />
@@ -255,19 +254,6 @@ describe('QueryBar Component', function () {
     });
   });
 
-  describe('when showQueryHistoryButton is false', function () {
-    beforeEach(function () {
-      renderQueryBar({
-        showQueryHistoryButton: false,
-      });
-    });
-
-    it('does not render the query history button', function () {
-      const queryHistoryButton = screen.queryByTestId(queryHistoryButtonId);
-      expect(queryHistoryButton).to.not.exist;
-    });
-  });
-
   describe('with three query options', function () {
     beforeEach(function () {
       renderQueryBar({
diff --git a/packages/compass-query-bar/src/components/query-bar.tsx b/packages/compass-query-bar/src/components/query-bar.tsx
index fc1767173a5..0c5d0d07119 100644
--- a/packages/compass-query-bar/src/components/query-bar.tsx
+++ b/packages/compass-query-bar/src/components/query-bar.tsx
@@ -146,7 +146,6 @@ type QueryBarProps = {
   filterHasContent: boolean;
   showExplainButton?: boolean;
   showExportToLanguageButton?: boolean;
-  showQueryHistoryButton?: boolean;
   valid: boolean;
   expanded: boolean;
   placeholders?: Record<QueryProperty, string>;
@@ -174,7 +173,6 @@ export const QueryBar: React.FunctionComponent<QueryBarProps> = ({
   filterHasContent,
   showExplainButton = false,
   showExportToLanguageButton = true,
-  showQueryHistoryButton = true,
   valid: isQueryValid,
   expanded: isQueryOptionsExpanded,
   placeholders,
@@ -225,6 +223,11 @@ export const QueryBar: React.FunctionComponent<QueryBarProps> = ({
     return filterHasContent;
   }, [isAIFeatureEnabled, isAIInputVisible, filterHasContent]);
 
+  const enableSavedAggregationsQueries = usePreference(
+    'enableSavedAggregationsQueries',
+    React
+  );
+
   return (
     <form
       className={cx(queryBarFormStyles, darkMode && queryBarFormDarkStyles)}
@@ -245,7 +248,7 @@ export const QueryBar: React.FunctionComponent<QueryBarProps> = ({
               Filter
             </Link>
           </Label>
-          {showQueryHistoryButton && <QueryHistoryButtonPopover />}
+          {enableSavedAggregationsQueries && <QueryHistoryButtonPopover />}
         </div>
         <div className={filterContainerStyles}>
           <QueryOptionComponent
diff --git a/packages/compass-query-bar/src/plugin.spec.tsx b/packages/compass-query-bar/src/plugin.spec.tsx
index 0ebd886ed4a..6e8099f5e11 100644
--- a/packages/compass-query-bar/src/plugin.spec.tsx
+++ b/packages/compass-query-bar/src/plugin.spec.tsx
@@ -6,6 +6,7 @@ import QueryBarPlugin from './plugin';
 import configureStore from './stores';
 import Sinon from 'sinon';
 import userEvent from '@testing-library/user-event';
+import preferencesAccess from 'compass-preferences-model';
 
 const mockQueryHistoryRole = {
   name: 'Query History',
@@ -55,18 +56,32 @@ describe('QueryBar [Plugin]', function () {
   });
 
   describe('when the plugin is rendered with or without a query history button', function () {
-    it('query history button renders by default', function () {
-      render(<QueryBarPlugin store={store} />);
-      expect(screen.getByTestId('query-history-button')).to.exist;
+    let enableSavedAggregationsQueries: boolean;
+
+    before(function () {
+      enableSavedAggregationsQueries =
+        preferencesAccess.getPreferences().enableSavedAggregationsQueries;
     });
 
-    it('query history button renders when showQueryHistoryButton prop is passed and set to true', function () {
-      render(<QueryBarPlugin store={store} showQueryHistoryButton />);
+    after(async function () {
+      await preferencesAccess.savePreferences({
+        enableSavedAggregationsQueries,
+      });
+    });
+
+    it('query history button renders when saved queries are enabled', async function () {
+      await preferencesAccess.savePreferences({
+        enableSavedAggregationsQueries: true,
+      });
+      render(<QueryBarPlugin store={store} />);
       expect(screen.getByTestId('query-history-button')).to.exist;
     });
 
-    it('query history button does not render when showQueryHistoryButton prop is passed and set to false', function () {
-      render(<QueryBarPlugin store={store} showQueryHistoryButton={false} />);
+    it('query history button does not render when ssaved queries are disabled', async function () {
+      await preferencesAccess.savePreferences({
+        enableSavedAggregationsQueries: false,
+      });
+      render(<QueryBarPlugin store={store} />);
       expect(screen.queryByTestId('query-history-button')).to.not.exist;
     });
   });