diff --git a/src/vs/base/browser/window.ts b/src/vs/base/browser/window.ts
index 46859b15efe..fe715d6f2c2 100644
--- a/src/vs/base/browser/window.ts
+++ b/src/vs/base/browser/window.ts
@@ -26,3 +26,13 @@ export const mainWindow = window as CodeWindow;
  * or `DOM.getActiveWindow()` to obtain the correct window for the context you are in.
  */
 export const $window = mainWindow;
+
+export function isAuxiliaryWindow(obj: Window): obj is CodeWindow {
+	if (obj === mainWindow) {
+		return false;
+	}
+
+	const candidate = obj as CodeWindow | undefined;
+
+	return typeof candidate?.vscodeWindowId === 'number';
+}
diff --git a/src/vs/workbench/browser/window.ts b/src/vs/workbench/browser/window.ts
index c32d69dd94d..2e76502326e 100644
--- a/src/vs/workbench/browser/window.ts
+++ b/src/vs/workbench/browser/window.ts
@@ -27,7 +27,7 @@ import { BrowserLifecycleService } from 'vs/workbench/services/lifecycle/browser
 import { ILifecycleService } from 'vs/workbench/services/lifecycle/common/lifecycle';
 import { IHostService } from 'vs/workbench/services/host/browser/host';
 import { registerWindowDriver } from 'vs/workbench/services/driver/browser/driver';
-import { CodeWindow, mainWindow } from 'vs/base/browser/window';
+import { CodeWindow, isAuxiliaryWindow, mainWindow } from 'vs/base/browser/window';
 import { createSingleCallFunction } from 'vs/base/common/functional';
 
 export abstract class BaseWindow extends Disposable {
@@ -71,6 +71,10 @@ export abstract class BaseWindow extends Disposable {
 			});
 
 			for (const { window, disposables } of dom.getWindows()) {
+				if (isAuxiliaryWindow(window) && window.document.visibilityState === 'hidden') {
+					continue; // skip over hidden windows (but never over main window)
+				}
+
 				const handle = (window as any).vscodeOriginalSetTimeout.apply(this, [handlerFn, timeout, ...args]);
 
 				const timeoutDisposable = toDisposable(() => {
diff --git a/src/vs/workbench/services/auxiliaryWindow/browser/auxiliaryWindowService.ts b/src/vs/workbench/services/auxiliaryWindow/browser/auxiliaryWindowService.ts
index a5cb6cb6d25..ecaad1817d0 100644
--- a/src/vs/workbench/services/auxiliaryWindow/browser/auxiliaryWindowService.ts
+++ b/src/vs/workbench/services/auxiliaryWindow/browser/auxiliaryWindowService.ts
@@ -110,16 +110,6 @@ class AuxiliaryWindow extends BaseWindow implements IAuxiliaryWindow {
 	}
 }
 
-export function isAuxiliaryWindow(obj: Window): obj is CodeWindow {
-	if (obj === mainWindow) {
-		return false;
-	}
-
-	const candidate = obj as CodeWindow | undefined;
-
-	return typeof candidate?.vscodeWindowId === 'number';
-}
-
 export class BrowserAuxiliaryWindowService extends Disposable implements IAuxiliaryWindowService {
 
 	declare readonly _serviceBrand: undefined;
@@ -208,7 +198,11 @@ export class BrowserAuxiliaryWindowService extends Disposable implements IAuxili
 		return auxiliaryWindow?.window;
 	}
 
-	protected createContainer(auxiliaryWindow: Window, disposables: DisposableStore): HTMLElement {
+	protected async resolveWindowId(auxiliaryWindow: Window): Promise<number> {
+		return BrowserAuxiliaryWindowService.WINDOW_IDS++;
+	}
+
+	protected createContainer(auxiliaryWindow: CodeWindow, disposables: DisposableStore): HTMLElement {
 		this.patchMethods(auxiliaryWindow);
 
 		this.applyMeta(auxiliaryWindow);
@@ -217,7 +211,7 @@ export class BrowserAuxiliaryWindowService extends Disposable implements IAuxili
 		return this.applyHTML(auxiliaryWindow, disposables);
 	}
 
-	protected patchMethods(auxiliaryWindow: Window): void {
+	protected patchMethods(auxiliaryWindow: CodeWindow): void {
 
 		// Disallow `createElement` because it would create
 		// HTML Elements in the "wrong" context and break
@@ -227,11 +221,7 @@ export class BrowserAuxiliaryWindowService extends Disposable implements IAuxili
 		};
 	}
 
-	protected async resolveWindowId(auxiliaryWindow: Window): Promise<number> {
-		return BrowserAuxiliaryWindowService.WINDOW_IDS++;
-	}
-
-	private applyMeta(auxiliaryWindow: Window): void {
+	private applyMeta(auxiliaryWindow: CodeWindow): void {
 		const metaCharset = createMetaElement(auxiliaryWindow.document.head);
 		metaCharset.setAttribute('charset', 'utf-8');
 
@@ -247,7 +237,7 @@ export class BrowserAuxiliaryWindowService extends Disposable implements IAuxili
 		}
 	}
 
-	protected applyCSS(auxiliaryWindow: Window, disposables: DisposableStore): void {
+	protected applyCSS(auxiliaryWindow: CodeWindow, disposables: DisposableStore): void {
 		mark('code/auxiliaryWindow/willApplyCSS');
 
 		const mapOriginalToClone = new Map<Node /* original */, Node /* clone */>();
@@ -313,7 +303,7 @@ export class BrowserAuxiliaryWindowService extends Disposable implements IAuxili
 		mark('code/auxiliaryWindow/didApplyCSS');
 	}
 
-	private applyHTML(auxiliaryWindow: Window, disposables: DisposableStore): HTMLElement {
+	private applyHTML(auxiliaryWindow: CodeWindow, disposables: DisposableStore): HTMLElement {
 		mark('code/auxiliaryWindow/willApplyHTML');
 
 		// Create workbench container and apply classes
diff --git a/src/vs/workbench/services/auxiliaryWindow/electron-sandbox/auxiliaryWindowService.ts b/src/vs/workbench/services/auxiliaryWindow/electron-sandbox/auxiliaryWindowService.ts
index d4cb8a37553..66427a0fe8c 100644
--- a/src/vs/workbench/services/auxiliaryWindow/electron-sandbox/auxiliaryWindowService.ts
+++ b/src/vs/workbench/services/auxiliaryWindow/electron-sandbox/auxiliaryWindowService.ts
@@ -31,6 +31,14 @@ export class NativeAuxiliaryWindowService extends BrowserAuxiliaryWindowService
 		super(layoutService, dialogService);
 	}
 
+	protected override async resolveWindowId(auxiliaryWindow: NativeAuxiliaryWindow): Promise<number> {
+		mark('code/auxiliaryWindow/willResolveWindowId');
+		const windowId = await auxiliaryWindow.vscode.ipcRenderer.invoke('vscode:registerAuxiliaryWindow', this.nativeHostService.windowId);
+		mark('code/auxiliaryWindow/didResolveWindowId');
+
+		return windowId;
+	}
+
 	protected override createContainer(auxiliaryWindow: NativeAuxiliaryWindow, disposables: DisposableStore): HTMLElement {
 
 		// Zoom level
@@ -41,14 +49,6 @@ export class NativeAuxiliaryWindowService extends BrowserAuxiliaryWindowService
 		return super.createContainer(auxiliaryWindow, disposables);
 	}
 
-	protected override async resolveWindowId(auxiliaryWindow: NativeAuxiliaryWindow): Promise<number> {
-		mark('code/auxiliaryWindow/willResolveWindowId');
-		const windowId = await auxiliaryWindow.vscode.ipcRenderer.invoke('vscode:registerAuxiliaryWindow', this.nativeHostService.windowId);
-		mark('code/auxiliaryWindow/didResolveWindowId');
-
-		return windowId;
-	}
-
 	protected override patchMethods(auxiliaryWindow: NativeAuxiliaryWindow): void {
 		super.patchMethods(auxiliaryWindow);
 
diff --git a/src/vs/workbench/services/host/browser/browserHostService.ts b/src/vs/workbench/services/host/browser/browserHostService.ts
index d8734794dc5..0bd525f2529 100644
--- a/src/vs/workbench/services/host/browser/browserHostService.ts
+++ b/src/vs/workbench/services/host/browser/browserHostService.ts
@@ -37,8 +37,7 @@ import { Schemas } from 'vs/base/common/network';
 import { ITextEditorOptions } from 'vs/platform/editor/common/editor';
 import { IUserDataProfileService } from 'vs/workbench/services/userDataProfile/common/userDataProfile';
 import { coalesce } from 'vs/base/common/arrays';
-import { isAuxiliaryWindow } from 'vs/workbench/services/auxiliaryWindow/browser/auxiliaryWindowService';
-import { mainWindow } from 'vs/base/browser/window';
+import { mainWindow, isAuxiliaryWindow } from 'vs/base/browser/window';
 
 /**
  * A workspace to open in the workbench can either be:
diff --git a/src/vs/workbench/services/host/electron-sandbox/nativeHostService.ts b/src/vs/workbench/services/host/electron-sandbox/nativeHostService.ts
index a012441c9f6..2b766c62887 100644
--- a/src/vs/workbench/services/host/electron-sandbox/nativeHostService.ts
+++ b/src/vs/workbench/services/host/electron-sandbox/nativeHostService.ts
@@ -14,9 +14,10 @@ import { Disposable } from 'vs/base/common/lifecycle';
 import { NativeHostService } from 'vs/platform/native/common/nativeHostService';
 import { INativeWorkbenchEnvironmentService } from 'vs/workbench/services/environment/electron-sandbox/environmentService';
 import { IMainProcessService } from 'vs/platform/ipc/common/mainProcessService';
-import { IAuxiliaryWindowService, isAuxiliaryWindow } from 'vs/workbench/services/auxiliaryWindow/browser/auxiliaryWindowService';
+import { IAuxiliaryWindowService } from 'vs/workbench/services/auxiliaryWindow/browser/auxiliaryWindowService';
 import { disposableWindowInterval, getActiveDocument, getWindowsCount, onDidRegisterWindow } from 'vs/base/browser/dom';
 import { memoize } from 'vs/base/common/decorators';
+import { isAuxiliaryWindow } from 'vs/base/browser/window';
 
 class WorkbenchNativeHostService extends NativeHostService {