diff --git a/src/App.tsx b/src/App.tsx
index 8e48f05e..5259db79 100644
--- a/src/App.tsx
+++ b/src/App.tsx
@@ -43,6 +43,8 @@ import { useLayoutPanels } from './hooks/useLayoutPanels'
 import { ConflictResolverModal } from './components/ConflictResolverModal'
 import { ConfirmDeleteDialog } from './components/ConfirmDeleteDialog'
 import { UpdateBanner } from './components/UpdateBanner'
+import { FlatVaultMigrationBanner } from './components/FlatVaultMigrationBanner'
+import { useFlatVaultMigration } from './hooks/useFlatVaultMigration'
 import { invoke } from '@tauri-apps/api/core'
 import { isTauri, mockInvoke } from './mock-tauri'
 import type { SidebarSelection, VaultEntry } from './types'
@@ -87,6 +89,7 @@ function App() {
   const { settings, saveSettings } = useSettings()
   const themeManager = useThemeManager(resolvedPath, vault.entries)
 
+  const flatVaultMigration = useFlatVaultMigration(resolvedPath, vault.entries.length > 0, vault.reloadVault)
   const { mcpStatus, installMcp } = useMcpStatus(resolvedPath, setToastMessage)
 
   const indexing = useIndexing(resolvedPath)
@@ -576,6 +579,17 @@ function App() {
           />
         </div>
       </div>
+      {flatVaultMigration.needsMigration && (
+        <FlatVaultMigrationBanner
+          strayFileCount={flatVaultMigration.strayFiles.length}
+          isMigrating={flatVaultMigration.isMigrating}
+          onMigrate={async () => {
+            const count = await flatVaultMigration.migrate()
+            setToastMessage(`Migrated ${count} file${count !== 1 ? 's' : ''} to vault root`)
+          }}
+          onDismiss={flatVaultMigration.dismiss}
+        />
+      )}
       <UpdateBanner status={updateStatus} actions={updateActions} />
       <StatusBar noteCount={vault.entries.length} modifiedCount={vault.modifiedFiles.length} vaultPath={vaultSwitcher.vaultPath} vaults={vaultSwitcher.allVaults} onSwitchVault={vaultSwitcher.switchVault} onOpenSettings={dialogs.openSettings} onOpenLocalFolder={vaultSwitcher.handleOpenLocalFolder} onConnectGitHub={dialogs.openGitHubVault} onClickPending={() => setSelection({ kind: 'filter', filter: 'changes' })} hasGitHub={!!settings.github_token} syncStatus={autoSync.syncStatus} lastSyncTime={autoSync.lastSyncTime} conflictCount={autoSync.conflictFiles.length} lastCommitInfo={autoSync.lastCommitInfo} onTriggerSync={autoSync.triggerSync} onOpenConflictResolver={handleOpenConflictResolver} zoomLevel={zoom.zoomLevel} onZoomReset={zoom.zoomReset} buildNumber={buildNumber} onCheckForUpdates={handleCheckForUpdates} indexingProgress={indexing.progress} lastIndexedTime={indexing.lastIndexedTime} onRetryIndexing={indexing.retryIndexing} onReindexVault={indexing.triggerFullReindex} onRemoveVault={vaultSwitcher.removeVault} mcpStatus={mcpStatus} onInstallMcp={installMcp} />
       <Toast message={toastMessage} onDismiss={() => setToastMessage(null)} />
diff --git a/src/components/FlatVaultMigrationBanner.tsx b/src/components/FlatVaultMigrationBanner.tsx
new file mode 100644
index 00000000..0b185636
--- /dev/null
+++ b/src/components/FlatVaultMigrationBanner.tsx
@@ -0,0 +1,37 @@
+interface FlatVaultMigrationBannerProps {
+  strayFileCount: number
+  isMigrating: boolean
+  onMigrate: () => void
+  onDismiss: () => void
+}
+
+/**
+ * Banner shown when the vault has files in non-protected subfolders.
+ * Offers to flatten them to the vault root.
+ */
+export function FlatVaultMigrationBanner({ strayFileCount, isMigrating, onMigrate, onDismiss }: FlatVaultMigrationBannerProps) {
+  return (
+    <div className="flex items-center gap-3 px-4 py-2 bg-amber-50 dark:bg-amber-950 border-b border-amber-200 dark:border-amber-800 text-sm" data-testid="migration-banner">
+      <span className="flex-1 text-amber-800 dark:text-amber-200">
+        {strayFileCount} note{strayFileCount !== 1 ? 's' : ''} found in subfolders.
+        Flatten to vault root for consistent scanning.
+      </span>
+      <button
+        className="px-3 py-1 text-xs font-medium rounded bg-amber-600 text-white hover:bg-amber-700 disabled:opacity-50"
+        onClick={onMigrate}
+        disabled={isMigrating}
+        data-testid="migration-flatten-btn"
+      >
+        {isMigrating ? 'Migrating...' : 'Flatten Now'}
+      </button>
+      <button
+        className="px-2 py-1 text-xs text-amber-600 dark:text-amber-400 hover:underline"
+        onClick={onDismiss}
+        disabled={isMigrating}
+        data-testid="migration-dismiss-btn"
+      >
+        Dismiss
+      </button>
+    </div>
+  )
+}
diff --git a/src/hooks/useFlatVaultMigration.ts b/src/hooks/useFlatVaultMigration.ts
new file mode 100644
index 00000000..b8982759
--- /dev/null
+++ b/src/hooks/useFlatVaultMigration.ts
@@ -0,0 +1,71 @@
+import { useState, useEffect, useCallback } from 'react'
+import { invoke } from '@tauri-apps/api/core'
+import { isTauri } from '../mock-tauri'
+
+interface HealthReport {
+  stray_files: string[]
+  title_mismatches: { path: string; filename: string; title: string; expected_filename: string }[]
+}
+
+interface FlatVaultMigration {
+  /** True if stray files were detected in non-protected subfolders. */
+  needsMigration: boolean
+  /** List of stray file paths (relative to vault root). */
+  strayFiles: string[]
+  /** Dismiss the migration prompt without migrating. */
+  dismiss: () => void
+  /** Run flatten_vault and reload. Returns the count of files moved. */
+  migrate: () => Promise<number>
+  /** True while migration is running. */
+  isMigrating: boolean
+}
+
+/**
+ * Detects if the vault has files in non-protected subfolders and offers
+ * to flatten them to the vault root. Runs once on vault load.
+ */
+export function useFlatVaultMigration(
+  vaultPath: string,
+  entriesLoaded: boolean,
+  reloadVault: () => Promise<void>,
+): FlatVaultMigration {
+  const [strayFiles, setStrayFiles] = useState<string[]>([])
+  const [dismissed, setDismissed] = useState(false)
+  const [isMigrating, setIsMigrating] = useState(false)
+
+  useEffect(() => {
+    if (!entriesLoaded || !vaultPath || !isTauri()) return
+    let cancelled = false
+    invoke<HealthReport>('vault_health_check', { vaultPath })
+      .then((report) => {
+        if (!cancelled && report.stray_files.length > 0) {
+          setStrayFiles(report.stray_files)
+        }
+      })
+      .catch(() => { /* non-critical */ })
+    return () => { cancelled = true }
+  }, [vaultPath, entriesLoaded])
+
+  const dismiss = useCallback(() => setDismissed(true), [])
+
+  const migrate = useCallback(async () => {
+    setIsMigrating(true)
+    try {
+      const count = await invoke<number>('flatten_vault', { vaultPath })
+      setStrayFiles([])
+      setDismissed(true)
+      await reloadVault()
+      return count
+    } finally {
+      setIsMigrating(false)
+    }
+  }, [vaultPath, reloadVault])
+
+  return {
+    needsMigration: strayFiles.length > 0 && !dismissed,
+    strayFiles,
+    dismiss,
+    migrate,
+    isMigrating,
+  }
+}