diff --git a/arduino-ide-extension/src/browser/contributions/burn-bootloader.ts b/arduino-ide-extension/src/browser/contributions/burn-bootloader.ts
index 2da1e20d..2ad15078 100644
--- a/arduino-ide-extension/src/browser/contributions/burn-bootloader.ts
+++ b/arduino-ide-extension/src/browser/contributions/burn-bootloader.ts
@@ -29,6 +29,7 @@ export class BurnBootloader extends CoreServiceContribution {
   }
 
   private async burnBootloader(): Promise<void> {
+    this.clearVisibleNotification();
     const options = await this.options();
     try {
       await this.doWithProgress({
diff --git a/arduino-ide-extension/src/browser/contributions/contribution.ts b/arduino-ide-extension/src/browser/contributions/contribution.ts
index d3ae285f..309a72db 100644
--- a/arduino-ide-extension/src/browser/contributions/contribution.ts
+++ b/arduino-ide-extension/src/browser/contributions/contribution.ts
@@ -59,6 +59,8 @@ import { ClipboardService } from '@theia/core/lib/browser/clipboard-service';
 import { ExecuteWithProgress } from '../../common/protocol/progressible';
 import { BoardsServiceProvider } from '../boards/boards-service-provider';
 import { BoardsDataStore } from '../boards/boards-data-store';
+import { NotificationManager } from '../theia/messages/notifications-manager';
+import { MessageType } from '@theia/core/lib/common/message-service-protocol';
 
 export {
   Command,
@@ -186,6 +188,22 @@ export abstract class CoreServiceContribution extends SketchContribution {
   @inject(ResponseServiceClient)
   private readonly responseService: ResponseServiceClient;
 
+  @inject(NotificationManager)
+  private readonly notificationManager: NotificationManager;
+
+  /**
+   * This is the internal (Theia) ID of the notification that is currently visible.
+   * It's stored here as a field to be able to close it before executing any new core command (such as verify, upload, etc.)
+   */
+  private visibleNotificationId: string | undefined;
+
+  protected clearVisibleNotification(): void {
+    if (this.visibleNotificationId) {
+      this.notificationManager.clear(this.visibleNotificationId);
+      this.visibleNotificationId = undefined;
+    }
+  }
+
   protected handleError(error: unknown): void {
     this.tryToastErrorMessage(error);
   }
@@ -208,6 +226,7 @@ export abstract class CoreServiceContribution extends SketchContribution {
         'arduino/coreContribution/copyError',
         'Copy error messages'
       );
+      this.visibleNotificationId = this.notificationId(message, copyAction);
       this.messageService.error(message, copyAction).then(async (action) => {
         if (action === copyAction) {
           const content = await this.outputChannelManager.contentOfChannel(
@@ -241,6 +260,14 @@ export abstract class CoreServiceContribution extends SketchContribution {
     });
     return result;
   }
+
+  private notificationId(message: string, ...actions: string[]): string {
+    return this.notificationManager.getMessageId({
+      text: message,
+      actions,
+      type: MessageType.Error,
+    });
+  }
 }
 
 export namespace Contribution {
diff --git a/arduino-ide-extension/src/browser/contributions/upload-sketch.ts b/arduino-ide-extension/src/browser/contributions/upload-sketch.ts
index e15e612a..d4bad139 100644
--- a/arduino-ide-extension/src/browser/contributions/upload-sketch.ts
+++ b/arduino-ide-extension/src/browser/contributions/upload-sketch.ts
@@ -191,6 +191,7 @@ export class UploadSketch extends CoreServiceContribution {
       // uploadInProgress will be set to false whether the upload fails or not
       this.uploadInProgress = true;
       this.onDidChangeEmitter.fire();
+      this.clearVisibleNotification();
 
       const verifyOptions =
         await this.commandService.executeCommand<CoreService.Options.Compile>(
diff --git a/arduino-ide-extension/src/browser/contributions/verify-sketch.ts b/arduino-ide-extension/src/browser/contributions/verify-sketch.ts
index 3fc2d53a..fe4de6f6 100644
--- a/arduino-ide-extension/src/browser/contributions/verify-sketch.ts
+++ b/arduino-ide-extension/src/browser/contributions/verify-sketch.ts
@@ -108,6 +108,7 @@ export class VerifySketch extends CoreServiceContribution {
         this.verifyInProgress = true;
         this.onDidChangeEmitter.fire();
       }
+      this.clearVisibleNotification();
       this.coreErrorHandler.reset();
 
       const options = await this.options(params?.exportBinaries);
diff --git a/arduino-ide-extension/src/browser/theia/messages/notifications-manager.ts b/arduino-ide-extension/src/browser/theia/messages/notifications-manager.ts
index c3842750..bdc1ed35 100644
--- a/arduino-ide-extension/src/browser/theia/messages/notifications-manager.ts
+++ b/arduino-ide-extension/src/browser/theia/messages/notifications-manager.ts
@@ -1,9 +1,10 @@
-import { injectable } from '@theia/core/shared/inversify';
 import { CancellationToken } from '@theia/core/lib/common/cancellation';
-import {
+import type {
+  Message,
   ProgressMessage,
   ProgressUpdate,
 } from '@theia/core/lib/common/message-service-protocol';
+import { injectable } from '@theia/core/shared/inversify';
 import { NotificationManager as TheiaNotificationManager } from '@theia/messages/lib/browser/notifications-manager';
 
 @injectable()
@@ -34,7 +35,9 @@ export class NotificationManager extends TheiaNotificationManager {
     this.fireUpdatedEvent();
   }
 
-  protected override toPlainProgress(update: ProgressUpdate): number | undefined {
+  protected override toPlainProgress(
+    update: ProgressUpdate
+  ): number | undefined {
     if (!update.work) {
       return undefined;
     }
@@ -43,4 +46,11 @@ export class NotificationManager extends TheiaNotificationManager {
     }
     return Math.min((update.work.done / update.work.total) * 100, 100);
   }
+
+  /**
+   * For `public` visibility.
+   */
+  override getMessageId(message: Message): string {
+    return super.getMessageId(message);
+  }
 }