diff --git a/packages/app-desktop/ElectronAppWrapper.ts b/packages/app-desktop/ElectronAppWrapper.ts
index 989c5be9b0..ba76b492bc 100644
--- a/packages/app-desktop/ElectronAppWrapper.ts
+++ b/packages/app-desktop/ElectronAppWrapper.ts
@@ -36,12 +36,21 @@ interface SecondaryWindowData {
 	electronId: number;
 }
 
+export interface Options {
+	env: string;
+	profilePath: string|null;
+	isDebugMode: boolean;
+	isEndToEndTesting: boolean;
+	initialCallbackUrl: string;
+}
+
 export default class ElectronAppWrapper {
 	private logger_: Logger = null;
 	private electronApp_: App;
 	private env_: string;
 	private isDebugMode_: boolean;
 	private profilePath_: string;
+	private isEndToEndTesting_: boolean;
 
 	private win_: BrowserWindow = null;
 	private mainWindowHidden_ = true;
@@ -65,12 +74,13 @@ export default class ElectronAppWrapper {
 
 	private ipcLogger_: Logger;
 
-	public constructor(electronApp: App, env: string, profilePath: string|null, isDebugMode: boolean, initialCallbackUrl: string) {
+	public constructor(electronApp: App, { env, profilePath, isDebugMode, initialCallbackUrl, isEndToEndTesting }: Options) {
 		this.electronApp_ = electronApp;
 		this.env_ = env;
 		this.isDebugMode_ = isDebugMode;
 		this.profilePath_ = profilePath;
 		this.initialCallbackUrl_ = initialCallbackUrl;
+		this.isEndToEndTesting_ = isEndToEndTesting;
 
 		this.profileLocker_ = new FileLocker(`${this.profilePath_}/lock`);
 
@@ -576,7 +586,9 @@ export default class ElectronAppWrapper {
 	}
 
 	public async ensureSingleInstance() {
-		// if (this.env_ === 'dev') return false;
+		// When end-to-end testing, multiple instances of Joplin are intentionally created at the same time,
+		// or very close to one another. The single instance handling logic can interfere with this, so disable it.
+		if (this.isEndToEndTesting_) return false;
 
 		interface OnSecondInstanceMessageData {
 			profilePath: string;
diff --git a/packages/app-desktop/integration-tests/util/createStartupArgs.ts b/packages/app-desktop/integration-tests/util/createStartupArgs.ts
index 60fcd5fad2..e499861a8a 100644
--- a/packages/app-desktop/integration-tests/util/createStartupArgs.ts
+++ b/packages/app-desktop/integration-tests/util/createStartupArgs.ts
@@ -7,7 +7,7 @@ const createStartupArgs = (profileDirectory: string) => {
 
 	// We need to run with --env dev to disable the single instance check.
 	return [
-		mainPath, '--env', 'dev', '--no-welcome', '--profile', resolve(profileDirectory),
+		mainPath, '--env', 'dev', '--no-welcome', '--running-tests', '--profile', resolve(profileDirectory),
 	];
 };
 
diff --git a/packages/app-desktop/main.js b/packages/app-desktop/main.js
index 32f1b1d99f..4d2f129f58 100644
--- a/packages/app-desktop/main.js
+++ b/packages/app-desktop/main.js
@@ -38,6 +38,7 @@ Logger.fsDriver_ = new FsDriverNode();
 const env = envFromArgs(process.argv);
 const profileFromArgs = getFlagValueFromArgs(process.argv, '--profile', null);
 const isDebugMode = !!process.argv && process.argv.indexOf('--debug') >= 0;
+const isEndToEndTesting = !!process.argv?.includes('--running-tests');
 const altInstanceId = getFlagValueFromArgs(process.argv, '--alt-instance-id', '');
 
 // We initialize all these variables here because they are needed from the main process. They are
@@ -64,7 +65,9 @@ void registerCustomProtocols();
 
 const initialCallbackUrl = process.argv.find((arg) => isCallbackUrl(arg));
 
-const wrapper = new ElectronAppWrapper(electronApp, env, rootProfileDir, isDebugMode, initialCallbackUrl);
+const wrapper = new ElectronAppWrapper(electronApp, {
+	env, profilePath: rootProfileDir, isDebugMode, initialCallbackUrl, isEndToEndTesting,
+});
 
 initBridge(wrapper, appId, appName, rootProfileDir, autoUploadCrashDumps, altInstanceId);
 
diff --git a/packages/lib/utils/processStartFlags.ts b/packages/lib/utils/processStartFlags.ts
index bda8456093..4f437cc7f6 100644
--- a/packages/lib/utils/processStartFlags.ts
+++ b/packages/lib/utils/processStartFlags.ts
@@ -188,6 +188,12 @@ const processStartFlags = async (argv: string[], setDefaults = true) => {
 			continue;
 		}
 
+		if (arg === '--running-tests') {
+			// Used by the desktop app to indicate that the app is running end-to-end tests.
+			argv.splice(0, 1);
+			continue;
+		}
+
 		if (arg.length && arg[0] === '-') {
 			throw new JoplinError(_('Unknown flag: %s', arg), 'flagError');
 		} else {