diff --git a/packages/desktop-app/src/lib/components/layout/app-shell.svelte b/packages/desktop-app/src/lib/components/layout/app-shell.svelte
index 27342ce5f..640ed77d7 100644
--- a/packages/desktop-app/src/lib/components/layout/app-shell.svelte
+++ b/packages/desktop-app/src/lib/components/layout/app-shell.svelte
@@ -191,8 +191,14 @@
         const folderPath = await importService.selectFolder();
         if (!folderPath) return;
 
+        // Track if we've received step 9 (complete) to know when to unsubscribe
+        let unsubProgress: (() => void) | null = null;
+        let importFailed = false;
+
         // Subscribe to progress updates - show step-based messages
-        const unsubProgress = importService.onProgress((event) => {
+        // NOTE: Phase 2 runs in background after importDirectory returns,
+        // so we must NOT unsubscribe until step 9 is received
+        unsubProgress = importService.onProgress(async (event) => {
           // Calculate overall progress based on step (9 steps total)
           // Steps 2-3 have per-file progress, others are single events
           let progress: number;
@@ -206,9 +212,18 @@
             progress = Math.round((event.step / 9) * 100);
           }
 
-          // Step 9 (complete) shows success message
+          // Step 9 (complete) shows success message and triggers cleanup
           if (event.step === 9) {
-            statusBar.success(event.message);
+            if (!importFailed) {
+              statusBar.success(event.message);
+            }
+            // Unsubscribe now that import is fully complete
+            if (unsubProgress) {
+              unsubProgress();
+              unsubProgress = null;
+            }
+            // Refresh collections after background import completes
+            await collectionsData.loadCollections();
           } else {
             statusBar.show(event.message, progress);
           }
@@ -220,20 +235,27 @@
             exclude_patterns: ['design-system', 'node_modules', '.git'],
           });
 
-          // The completion message is now handled by the progress event (step 9)
-          // But if there were failures, show an error message
+          // Phase 1 complete - Phase 2 runs in background
+          // If there were parsing failures, show error (but don't override progress)
           if (result.failed > 0) {
+            importFailed = true;
             statusBar.error(`Import complete: ${result.successful} imported, ${result.failed} failed`);
+            // Unsubscribe since we're showing error
+            if (unsubProgress) {
+              unsubProgress();
+              unsubProgress = null;
+            }
           }
-
-          // Refresh collections after import
-          const { collectionsData } = await import('$lib/stores/collections');
-          await collectionsData.loadCollections();
+          // NOTE: Do NOT unsubProgress here - Phase 2 still running
         } catch (error) {
           log.error('Import failed', error);
+          importFailed = true;
           statusBar.error('Import failed: ' + (error instanceof Error ? error.message : String(error)));
-        } finally {
-          unsubProgress();
+          // Unsubscribe on error
+          if (unsubProgress) {
+            unsubProgress();
+            unsubProgress = null;
+          }
         }
       });
 
diff --git a/packages/desktop-app/src/lib/services/import-service.ts b/packages/desktop-app/src/lib/services/import-service.ts
index 3f8183375..664cc8c5b 100644
--- a/packages/desktop-app/src/lib/services/import-service.ts
+++ b/packages/desktop-app/src/lib/services/import-service.ts
@@ -101,6 +101,11 @@ class ImportService {
 
   /**
    * Import all markdown files from a directory
+   *
+   * NOTE: This method returns after Phase 1 (parsing) completes, but Phase 2
+   * (database operations) continues in background. Progress events will continue
+   * to be emitted until step 9 (complete). Callers should NOT unsubscribe from
+   * progress until they receive the step 9 event.
    */
   async importDirectory(
     directoryPath: string,
@@ -108,27 +113,25 @@ class ImportService {
   ): Promise<BatchImportResult> {
     log.info('Starting directory import', { path: directoryPath, options });
 
-    // Set up progress listener
+    // Set up progress listener (kept alive for background Phase 2)
     await this.setupProgressListener();
 
-    try {
-      const result = await invoke<BatchImportResult>('import_markdown_directory', {
-        directoryPath,
-        options: options || {},
-      });
+    const result = await invoke<BatchImportResult>('import_markdown_directory', {
+      directoryPath,
+      options: options || {},
+    });
 
-      log.info('Directory import complete', {
-        total: result.total_files,
-        successful: result.successful,
-        failed: result.failed,
-        duration_ms: result.duration_ms,
-      });
+    log.info('Directory import Phase 1 complete (Phase 2 running in background)', {
+      total: result.total_files,
+      successful: result.successful,
+      failed: result.failed,
+      duration_ms: result.duration_ms,
+    });
 
-      return result;
-    } finally {
-      // Clean up progress listener
-      this.teardownProgressListener();
-    }
+    // NOTE: Do NOT teardown listener here - Phase 2 is still running in background
+    // The listener will be cleaned up when the caller unsubscribes after step 9
+
+    return result;
   }
 
   /**