diff --git a/src/screens/REPL.tsx b/src/screens/REPL.tsx
index 1ee59943..bcfd6a4d 100644
--- a/src/screens/REPL.tsx
+++ b/src/screens/REPL.tsx
@@ -238,6 +238,7 @@ import { usePromptsFromClaudeInChrome } from 'src/hooks/usePromptsFromClaudeInCh
 import { getTipToShowOnSpinner, recordShownTip } from 'src/services/tips/tipScheduler.js';
 import type { Theme } from 'src/utils/theme.js';
 import { isPromptTypingSuppressionActive } from './replInputSuppression.js';
+import { shouldRunStartupChecks, STARTUP_CHECK_DELAY_MS } from './replStartupGates.js';
 import { checkAndDisableBypassPermissionsIfNeeded, checkAndDisableAutoModeIfNeeded, useKickOffCheckAndDisableBypassPermissionsIfNeeded, useKickOffCheckAndDisableAutoModeIfNeeded } from 'src/utils/permissions/bypassPermissionsKillswitch.js';
 import { SandboxManager } from 'src/utils/sandbox/sandbox-adapter.js';
 import { SANDBOX_NETWORK_ACCESS_TOOL_NAME } from 'src/cli/structuredIO.js';
@@ -792,10 +793,20 @@ export function REPL({
   // accepts, and only then is the REPL component mounted and this effect runs.
   // This ensures that plugin installations from repository and user settings only
   // happen after explicit user consent to trust the current working directory.
+  // We defer startup checks by STARTUP_CHECK_DELAY_MS and gate on
+  // promptTypingSuppressionActive so that plugin loading doesn't steal focus
+  // from the prompt during the vulnerable startup window (issue #363).
+  const startupChecksStartedRef = React.useRef(false)
   useEffect(() => {
-    if (isRemoteSession) return;
-    void performStartupChecks(setAppState);
-  }, [setAppState, isRemoteSession]);
+    if (isRemoteSession) return
+    if (startupChecksStartedRef.current) return
+    const timer = setTimeout(() => {
+      if (!shouldRunStartupChecks(isRemoteSession, startupChecksStartedRef.current, promptTypingSuppressionActive)) return
+      startupChecksStartedRef.current = true
+      void performStartupChecks(setAppState)
+    }, STARTUP_CHECK_DELAY_MS)
+    return () => clearTimeout(timer)
+  }, [setAppState, isRemoteSession, promptTypingSuppressionActive])
 
   // Allow Claude in Chrome MCP to send prompts through MCP notifications
   // and sync permission mode changes to the Chrome extension
@@ -2061,13 +2072,14 @@ export function REPL({
     if (allowDialogsWithAnimation && showRemoteCallout) return 'remote-callout';
 
     // LSP plugin recommendation (lowest priority - non-blocking suggestion)
-    if (allowDialogsWithAnimation && lspRecommendation) return 'lsp-recommendation';
+  // Suppress during startup window to prevent stealing focus from the prompt (issue #363)
+  if (allowDialogsWithAnimation && lspRecommendation && startupChecksStartedRef.current) return 'lsp-recommendation';
 
-    // Plugin hint from CLI/SDK stderr (same priority band as LSP rec)
-    if (allowDialogsWithAnimation && hintRecommendation) return 'plugin-hint';
+  // Plugin hint from CLI/SDK stderr (same priority band as LSP rec)
+  if (allowDialogsWithAnimation && hintRecommendation && startupChecksStartedRef.current) return 'plugin-hint';
 
-    // Desktop app upsell (max 3 launches, lowest priority)
-    if (allowDialogsWithAnimation && showDesktopUpsellStartup) return 'desktop-upsell';
+  // Desktop app upsell (max 3 launches, lowest priority)
+  if (allowDialogsWithAnimation && showDesktopUpsellStartup && startupChecksStartedRef.current) return 'desktop-upsell';
     return undefined;
   }
   const focusedInputDialog = getFocusedInputDialog();
diff --git a/src/screens/replStartupGates.test.ts b/src/screens/replStartupGates.test.ts
new file mode 100644
index 00000000..cd4ae96a
--- /dev/null
+++ b/src/screens/replStartupGates.test.ts
@@ -0,0 +1,32 @@
+import { describe, expect, test } from 'bun:test'
+
+import { shouldRunStartupChecks, STARTUP_CHECK_DELAY_MS } from './replStartupGates.js'
+
+describe('shouldRunStartupChecks', () => {
+  test('runs checks when not remote, not started, and not typing', () => {
+    expect(shouldRunStartupChecks(false, false, false)).toBe(true)
+  })
+
+  test('skips checks in remote sessions', () => {
+    expect(shouldRunStartupChecks(true, false, false)).toBe(false)
+  })
+
+  test('skips checks if already started', () => {
+    expect(shouldRunStartupChecks(false, true, false)).toBe(false)
+  })
+
+  test('skips checks while user is typing', () => {
+    expect(shouldRunStartupChecks(false, false, true)).toBe(false)
+  })
+
+  test('skips checks when remote even if started and typing', () => {
+    expect(shouldRunStartupChecks(true, true, true)).toBe(false)
+  })
+})
+
+describe('STARTUP_CHECK_DELAY_MS', () => {
+  test('delay is positive and reasonable', () => {
+    expect(STARTUP_CHECK_DELAY_MS).toBeGreaterThan(0)
+    expect(STARTUP_CHECK_DELAY_MS).toBeLessThanOrEqual(5000)
+  })
+})
\ No newline at end of file
diff --git a/src/screens/replStartupGates.ts b/src/screens/replStartupGates.ts
new file mode 100644
index 00000000..6f43ae5a
--- /dev/null
+++ b/src/screens/replStartupGates.ts
@@ -0,0 +1,27 @@
+/**
+ * Startup gates for the REPL.
+ *
+ * Prevents startup plugin checks and recommendation dialogs from stealing
+ * focus while the user is typing or has early input buffered.
+ *
+ * This addresses the root cause of issue #363: on mount, performStartupChecks
+ * triggers plugin loading, which populates trackedFiles, which triggers
+ * useLspPluginRecommendation to surface an LSP recommendation dialog. Since
+ * promptTypingSuppressionActive is false before the user has typed anything,
+ * getFocusedInputDialog() returns the dialog, unmounting PromptInput entirely.
+ */
+
+const STARTUP_CHECK_DELAY_MS = 1500
+
+export function shouldRunStartupChecks(
+  isRemoteSession: boolean,
+  hasStarted: boolean,
+  promptTypingSuppressionActive: boolean,
+): boolean {
+  if (isRemoteSession) return false
+  if (hasStarted) return false
+  if (promptTypingSuppressionActive) return false
+  return true
+}
+
+export { STARTUP_CHECK_DELAY_MS }
\ No newline at end of file