diff --git a/apps/ui/src/components/views/board-view.tsx b/apps/ui/src/components/views/board-view.tsx
index b4c050f6..028f7bd1 100644
--- a/apps/ui/src/components/views/board-view.tsx
+++ b/apps/ui/src/components/views/board-view.tsx
@@ -114,6 +114,11 @@ export function BoardView() {
   const pipelineConfigByProject = useAppStore((state) => state.pipelineConfigByProject);
   // Subscribe to worktreePanelVisibleByProject to trigger re-renders when it changes
   const worktreePanelVisibleByProject = useAppStore((state) => state.worktreePanelVisibleByProject);
+  // Subscribe to showInitScriptIndicatorByProject to trigger re-renders when it changes
+  const showInitScriptIndicatorByProject = useAppStore(
+    (state) => state.showInitScriptIndicatorByProject
+  );
+  const getShowInitScriptIndicator = useAppStore((state) => state.getShowInitScriptIndicator);
   const shortcuts = useKeyboardShortcutsConfig();
   const {
     features: hookFeatures,
@@ -1577,7 +1582,9 @@ export function BoardView() {
       />
 
       {/* Init Script Indicator - floating overlay for worktree init script status */}
-      <InitScriptIndicator projectPath={currentProject.path} />
+      {getShowInitScriptIndicator(currentProject.path) && (
+        <InitScriptIndicator projectPath={currentProject.path} />
+      )}
     </div>
   );
 }
diff --git a/apps/ui/src/components/views/settings-view/worktrees/worktrees-section.tsx b/apps/ui/src/components/views/settings-view/worktrees/worktrees-section.tsx
index 8a615c58..01ff77c6 100644
--- a/apps/ui/src/components/views/settings-view/worktrees/worktrees-section.tsx
+++ b/apps/ui/src/components/views/settings-view/worktrees/worktrees-section.tsx
@@ -3,7 +3,16 @@ import { Label } from '@/components/ui/label';
 import { Checkbox } from '@/components/ui/checkbox';
 import { Button } from '@/components/ui/button';
 import { ShellSyntaxEditor } from '@/components/ui/shell-syntax-editor';
-import { GitBranch, Terminal, FileCode, Save, RotateCcw, Trash2, Loader2 } from 'lucide-react';
+import {
+  GitBranch,
+  Terminal,
+  FileCode,
+  Save,
+  RotateCcw,
+  Trash2,
+  Loader2,
+  PanelBottomClose,
+} from 'lucide-react';
 import { cn } from '@/lib/utils';
 import { apiPost, apiPut, apiDelete } from '@/lib/api-fetch';
 import { toast } from 'sonner';
@@ -24,6 +33,8 @@ interface InitScriptResponse {
 
 export function WorktreesSection({ useWorktrees, onUseWorktreesChange }: WorktreesSectionProps) {
   const currentProject = useAppStore((s) => s.currentProject);
+  const getShowInitScriptIndicator = useAppStore((s) => s.getShowInitScriptIndicator);
+  const setShowInitScriptIndicator = useAppStore((s) => s.setShowInitScriptIndicator);
   const [scriptContent, setScriptContent] = useState('');
   const [originalContent, setOriginalContent] = useState('');
   const [scriptExists, setScriptExists] = useState(false);
@@ -31,6 +42,11 @@ export function WorktreesSection({ useWorktrees, onUseWorktreesChange }: Worktre
   const [isSaving, setIsSaving] = useState(false);
   const [isDeleting, setIsDeleting] = useState(false);
 
+  // Get the current show indicator setting
+  const showIndicator = currentProject?.path
+    ? getShowInitScriptIndicator(currentProject.path)
+    : true;
+
   // Check if there are unsaved changes
   const hasChanges = scriptContent !== originalContent;
 
@@ -181,6 +197,35 @@ export function WorktreesSection({ useWorktrees, onUseWorktreesChange }: Worktre
           </div>
         </div>
 
+        {/* Show Init Script Indicator Toggle */}
+        {currentProject && (
+          <div className="group flex items-start space-x-3 p-3 rounded-xl hover:bg-accent/30 transition-colors duration-200 -mx-3 mt-4">
+            <Checkbox
+              id="show-init-script-indicator"
+              checked={showIndicator}
+              onCheckedChange={(checked) => {
+                if (currentProject?.path) {
+                  setShowInitScriptIndicator(currentProject.path, checked === true);
+                }
+              }}
+              className="mt-1"
+            />
+            <div className="space-y-1.5">
+              <Label
+                htmlFor="show-init-script-indicator"
+                className="text-foreground cursor-pointer font-medium flex items-center gap-2"
+              >
+                <PanelBottomClose className="w-4 h-4 text-brand-500" />
+                Show Init Script Indicator
+              </Label>
+              <p className="text-xs text-muted-foreground/80 leading-relaxed">
+                Display a floating panel in the bottom-right corner showing init script execution
+                status and output when a worktree is created.
+              </p>
+            </div>
+          </div>
+        )}
+
         {/* Separator */}
         <div className="border-t border-border/30" />
 
diff --git a/apps/ui/src/store/app-store.ts b/apps/ui/src/store/app-store.ts
index 5479c015..974ffe87 100644
--- a/apps/ui/src/store/app-store.ts
+++ b/apps/ui/src/store/app-store.ts
@@ -665,6 +665,10 @@ export interface AppState {
   // Whether the worktree panel row is visible (default: true)
   worktreePanelVisibleByProject: Record<string, boolean>;
 
+  // Init Script Indicator Visibility (per-project, keyed by project path)
+  // Whether to show the floating init script indicator panel (default: true)
+  showInitScriptIndicatorByProject: Record<string, boolean>;
+
   // UI State (previously in localStorage, now synced via API)
   /** Whether worktree panel is collapsed in board view */
   worktreePanelCollapsed: boolean;
@@ -1078,6 +1082,10 @@ export interface AppActions {
   setWorktreePanelVisible: (projectPath: string, visible: boolean) => void;
   getWorktreePanelVisible: (projectPath: string) => boolean;
 
+  // Init Script Indicator Visibility actions (per-project)
+  setShowInitScriptIndicator: (projectPath: string, visible: boolean) => void;
+  getShowInitScriptIndicator: (projectPath: string) => boolean;
+
   // UI State actions (previously in localStorage, now synced via API)
   setWorktreePanelCollapsed: (collapsed: boolean) => void;
   setLastProjectDir: (dir: string) => void;
@@ -1208,6 +1216,7 @@ const initialState: AppState = {
   codexModelsLastFetched: null,
   pipelineConfigByProject: {},
   worktreePanelVisibleByProject: {},
+  showInitScriptIndicatorByProject: {},
   // UI State (previously in localStorage, now synced via API)
   worktreePanelCollapsed: false,
   lastProjectDir: '',
@@ -3124,6 +3133,21 @@ export const useAppStore = create<AppState & AppActions>()((set, get) => ({
     return get().worktreePanelVisibleByProject[projectPath] ?? true;
   },
 
+  // Init Script Indicator Visibility actions (per-project)
+  setShowInitScriptIndicator: (projectPath, visible) => {
+    set({
+      showInitScriptIndicatorByProject: {
+        ...get().showInitScriptIndicatorByProject,
+        [projectPath]: visible,
+      },
+    });
+  },
+
+  getShowInitScriptIndicator: (projectPath) => {
+    // Default to true (visible) if not set
+    return get().showInitScriptIndicatorByProject[projectPath] ?? true;
+  },
+
   // UI State actions (previously in localStorage, now synced via API)
   setWorktreePanelCollapsed: (collapsed) => set({ worktreePanelCollapsed: collapsed }),
   setLastProjectDir: (dir) => set({ lastProjectDir: dir }),
diff --git a/libs/types/src/settings.ts b/libs/types/src/settings.ts
index 07b4290d..7a46d4aa 100644
--- a/libs/types/src/settings.ts
+++ b/libs/types/src/settings.ts
@@ -595,6 +595,8 @@ export interface ProjectSettings {
   // UI Visibility
   /** Whether the worktree panel row is visible (default: true) */
   worktreePanelVisible?: boolean;
+  /** Whether to show the init script indicator panel (default: true) */
+  showInitScriptIndicator?: boolean;
 
   // Session Tracking
   /** Last chat session selected in this project */