diff --git a/apps/server/src/project/ProjectSetupScriptRunner.test.ts b/apps/server/src/project/ProjectSetupScriptRunner.test.ts
new file mode 100644
index 0000000000000..c295a06ac39ac
--- /dev/null
+++ b/apps/server/src/project/ProjectSetupScriptRunner.test.ts
@@ -0,0 +1,168 @@
+import * as NodeCrypto from "@effect/platform-node/NodeCrypto";
+import { describe, expect, it } from "@effect/vitest";
+import { ProjectId, type TerminalEvent, type TerminalSessionSnapshot } from "@t3tools/contracts";
+import * as HostProcess from "@t3tools/shared/HostProcess";
+import * as Deferred from "effect/Deferred";
+import * as Effect from "effect/Effect";
+import * as Fiber from "effect/Fiber";
+import * as Layer from "effect/Layer";
+import * as Queue from "effect/Queue";
+import { TestClock } from "effect/testing";
+
+import * as ServerSettings from "../serverSettings.ts";
+import * as TerminalManager from "../terminal/Manager.ts";
+import * as ProjectService from "./ProjectService.ts";
+import * as ProjectSetupScriptRunner from "./ProjectSetupScriptRunner.ts";
+
+const threadId = "thread-1";
+const terminalId = "setup-setup";
+const event = { threadId, terminalId, sequence: 1, createdAt: "2026-01-01T00:00:00.000Z" };
+
+const openSnapshot = (history: string): TerminalSessionSnapshot => ({
+  threadId,
+  terminalId,
+  cwd: "/repo/.t3/worktrees/feature",
+  worktreePath: null,
+  status: "running",
+  pid: 123,
+  history,
+  exitCode: null,
+  exitSignal: null,
+  label: "zsh",
+  updatedAt: "2026-01-01T00:00:00.000Z",
+});
+
+const makeHarness = Effect.fn(function* (options: {
+  readonly history?: string;
+  readonly opening?: Deferred.Deferred<void>;
+}) {
+  const listeners = new Set<(event: TerminalEvent) => Effect.Effect<void>>();
+  const writes = yield* Queue.unbounded<string>();
+  const outputLines = yield* Queue.unbounded<string>();
+  const terminals = Layer.mock(TerminalManager.TerminalManager)({
+    open: () =>
+      (options.opening
+        ? Deferred.succeed(options.opening, undefined).pipe(Effect.andThen(Effect.never))
+        : Effect.void
+      ).pipe(Effect.as(openSnapshot(options.history ?? ""))),
+    subscribe: (listener) =>
+      Effect.sync(() => {
+        listeners.add(listener);
+        return () => listeners.delete(listener);
+      }),
+    write: (input) => Queue.offer(writes, input.data).pipe(Effect.asVoid),
+    closeIdle: () => Effect.void,
+  });
+  const runner = yield* ProjectSetupScriptRunner.make.pipe(
+    Effect.provide(
+      Layer.mergeAll(
+        terminals,
+        Layer.mock(ProjectService.ProjectService)({}),
+        ServerSettings.layerTest(),
+        NodeCrypto.layer,
+      ),
+    ),
+    Effect.provideService(HostProcess.Platform, "darwin"),
+    Effect.provideService(HostProcess.Environment, { SHELL: "/bin/zsh" }),
+  );
+  const start = runner.runForThread({
+    threadId,
+    worktreePath: "/repo/.t3/worktrees/feature",
+    observeCompletion: { onOutputLine: (line) => Queue.offer(outputLines, line) },
+    project: {
+      id: ProjectId.make("project-1"),
+      workspaceRoot: "/repo",
+      scripts: [
+        {
+          id: "setup",
+          name: "Setup",
+          command: "vp i",
+          icon: "configure",
+          runOnWorktreeCreate: true,
+        },
+      ],
+    },
+  });
+  const emit = (terminalEvent: TerminalEvent) =>
+    Effect.forEach([...listeners], (listener) => listener(terminalEvent), { discard: true });
+  return { start, listeners, writes, outputLines, emit };
+});
+
+const setup = Effect.fn(function* (options: { readonly history?: string } = {}) {
+  const harness = yield* makeHarness(options);
+  const result = yield* harness.start;
+  const completion = result.status === "started" ? result.completion : undefined;
+  if (!completion) return yield* Effect.die("setup did not start an observed run");
+  return { ...harness, result, completion };
+});
+
+describe("ProjectSetupScriptRunner", () => {
+  it.effect("shows a startup prompt and types only once the line editor starts", () =>
+    Effect.gen(function* () {
+      const { result, writes, outputLines, emit } = yield* setup();
+      expect(result).toMatchObject({ status: "started", terminalId });
+
+      yield* emit({ ...event, type: "output", data: "Missing Node.\r\nInstall it? [y/N]: " });
+      yield* emit({ ...event, type: "activity", hasRunningSubprocess: true, label: "fnm" });
+      yield* TestClock.adjust("1 minute");
+      expect(yield* Queue.size(writes)).toBe(0);
+      expect(yield* Queue.takeAll(outputLines)).toEqual(["Missing Node.", "Install it? [y/N]:"]);
+
+      yield* emit({ ...event, type: "activity", hasRunningSubprocess: false, label: "zsh" });
+      yield* emit({ ...event, type: "output", data: "\r\n% \x1b[?2004h" });
+      expect(yield* Queue.take(writes)).toMatch(/^ \( vp i\r\);/);
+    }),
+  );
+
+  it.effect("types into a quiet shell that has no line editor", () =>
+    Effect.gen(function* () {
+      const { writes } = yield* setup();
+      yield* TestClock.adjust("3 seconds");
+      expect(yield* Queue.take(writes)).toMatch(/^ \( vp i\r\);/);
+    }),
+  );
+
+  it.effect("ignores line editor state restored from an earlier shell", () =>
+    Effect.gen(function* () {
+      const { writes, emit } = yield* setup({ history: "old run\r\n% \x1b[?2004h" });
+      yield* emit({ ...event, type: "activity", hasRunningSubprocess: true, label: "fnm" });
+      yield* TestClock.adjust("1 minute");
+      expect(yield* Queue.size(writes)).toBe(0);
+    }),
+  );
+
+  it.effect("forgets a busy startup child when the shell restarts", () =>
+    Effect.gen(function* () {
+      const { writes, emit } = yield* setup();
+      yield* emit({ ...event, type: "activity", hasRunningSubprocess: true, label: "fnm" });
+      yield* TestClock.adjust("1 minute");
+      expect(yield* Queue.size(writes)).toBe(0);
+      yield* emit({ ...event, type: "restarted", snapshot: openSnapshot("") });
+      // The restart lands inside a quiet window, so the next full window decides.
+      yield* TestClock.adjust("6 seconds");
+      expect(yield* Queue.take(writes)).toMatch(/^ \( vp i\r\);/);
+    }),
+  );
+
+  it.effect("drops its terminal listeners when cancelled while the terminal opens", () =>
+    Effect.gen(function* () {
+      const opening = yield* Deferred.make<void>();
+      const { start, listeners } = yield* makeHarness({ opening });
+      const fiber = yield* Effect.forkChild(start);
+      yield* Deferred.await(opening);
+      expect(listeners.size).toBe(2);
+      yield* Fiber.interrupt(fiber);
+      expect(listeners.size).toBe(0);
+    }),
+  );
+
+  it.effect("does not type into a shell that exits during startup", () =>
+    Effect.gen(function* () {
+      const { completion, writes, emit } = yield* setup();
+      yield* emit({ ...event, type: "exited", exitCode: 1, exitSignal: null });
+      expect(yield* completion).toMatchObject({ exitCode: null });
+      yield* TestClock.adjust("1 minute");
+      expect(yield* Queue.size(writes)).toBe(0);
+    }),
+  );
+});
diff --git a/apps/server/src/project/ProjectSetupScriptRunner.ts b/apps/server/src/project/ProjectSetupScriptRunner.ts
index da8bb9a6c56a9..a2f8e0fc8e201 100644
--- a/apps/server/src/project/ProjectSetupScriptRunner.ts
+++ b/apps/server/src/project/ProjectSetupScriptRunner.ts
@@ -74,7 +74,7 @@ export class ProjectSetupScriptOperationError extends Schema.TaggedError<Project
     projectId: Schema.optional(Schema.String),
     projectCwd: Schema.optional(Schema.String),
     worktreePath: Schema.String,
-    operation: Schema.Literals(["resolveProject", "readSettings", "openTerminal", "writeCommand"]),
+    operation: Schema.Literals(["resolveProject", "readSettings", "openTerminal"]),
     cause: Schema.Defect(),
   },
 ) {
@@ -139,6 +139,18 @@ function stripTerminalControl(text: string): string {
   );
 }
 
+// Line editors (zsh, fish, bash 5.1+) enable bracketed paste when they start reading a command.
+const BRACKETED_PASTE_ON = "\x1b[?2004h";
+const BRACKETED_PASTE_OFF = "\x1b[?2004l";
+// Longer than one subprocess poll plus its ps timeout, so a startup prompt is seen as busy first.
+const SHELL_QUIET_FALLBACK = "3 seconds";
+
+function lineEditorReading(text: string, previous: boolean): boolean {
+  const on = text.lastIndexOf(BRACKETED_PASTE_ON);
+  const off = text.lastIndexOf(BRACKETED_PASTE_OFF);
+  return on === off ? previous : on > off;
+}
+
 type CompletionShell = "posix" | "fish" | "powershell";
 
 function resolveCompletionShell(
@@ -176,6 +188,7 @@ export const make = Effect.gen(function* () {
   const terminalManager = yield* TerminalManager.TerminalManager;
   const serverSettings = yield* ServerSettings.ServerSettingsService;
   const crypto = yield* Crypto.Crypto;
+  const serviceScope = yield* Effect.scope;
   const completionShell = resolveCompletionShell(
     yield* HostProcess.Platform,
     yield* HostProcess.Environment,
@@ -263,7 +276,67 @@ export const make = Effect.gen(function* () {
         Effect.tap(() => Deferred.await(promptReturned).pipe(Effect.timeoutOption("1 second"))),
         Effect.ensuring(Effect.sync(() => unsubscribe())),
       );
-      return { completion, unsubscribe };
+      // A startup prompt waits for input on a line that has no newline yet.
+      const flushPartialLine = Effect.suspend(() => {
+        const partial = lineBuffer;
+        lineBuffer = "";
+        return handleLine(partial);
+      });
+      const abandon = settle(null).pipe(
+        Effect.andThen(Deferred.succeed(promptReturned, undefined)),
+      );
+      return { completion, unsubscribe, flushPartialLine, abandon };
+    },
+  );
+
+  // Input typed during shell startup can be read by an rc-file prompt (fnm, nvm) instead of the
+  // shell, which loses the command. Subscribe before the terminal opens so no activity is missed.
+  const watchShellReadiness = Effect.fn("ProjectSetupScriptRunner.watchShellReadiness")(
+    function* (input: {
+      readonly threadId: string;
+      readonly terminalId: string;
+      readonly onStartupPrompt: Effect.Effect<void>;
+    }) {
+      const outcome = yield* Deferred.make<"ready" | "exited">();
+      let reading = false;
+      let carry = "";
+      let busy = false;
+      let activity = 0;
+      const unsubscribe = yield* terminalManager.subscribe((event) => {
+        if (event.threadId !== input.threadId || event.terminalId !== input.terminalId) {
+          return Effect.void;
+        }
+        activity += 1;
+        // A new shell process starts idle; the manager resets its subprocess state without an event.
+        if (event.type === "started" || event.type === "restarted") {
+          busy = false;
+          reading = false;
+          carry = "";
+        }
+        if (event.type === "activity") busy = event.hasRunningSubprocess;
+        if (event.type === "output") {
+          const text = carry + event.data;
+          carry = text.slice(-(BRACKETED_PASTE_ON.length - 1));
+          reading = lineEditorReading(text, reading);
+        }
+        if (event.type === "exited" || event.type === "closed") {
+          return Deferred.succeed(outcome, "exited").pipe(Effect.asVoid);
+        }
+        return reading ? Deferred.succeed(outcome, "ready").pipe(Effect.asVoid) : Effect.void;
+      });
+      // A startup prompt runs as a child process, so a busy shell keeps waiting for the user.
+      const quiet = Effect.gen(function* () {
+        while (true) {
+          const seen = activity;
+          yield* Effect.sleep(SHELL_QUIET_FALLBACK);
+          if (activity !== seen) continue;
+          if (!busy) return "ready" as const;
+          yield* input.onStartupPrompt;
+        }
+      });
+      // Restored history can hold a previous shell's line editor state, so only live output counts.
+      const wait = Deferred.await(outcome).pipe(Effect.raceFirst(quiet));
+      return { wait, unsubscribe };
     },
   );
 
@@ -361,25 +434,7 @@ export const make = Effect.gen(function* () {
           )
         : script.command;
 
-    yield* terminalManager
-      .open({
-        threadId: input.threadId,
-        terminalId,
-        cwd,
-        worktreePath: input.worktreePath,
-        env: { ...env, NO_COLOR: "1", FORCE_COLOR: "0" },
-      })
-      .pipe(
-        Effect.mapError(
-          (cause) =>
-            new ProjectSetupScriptOperationError({
-              ...errorContext,
-              operation: "openTerminal",
-              cause,
-            }),
-        ),
-      );
-    // Subscribe before writing so the sentinel cannot race past the listener.
+    // Subscribe before opening so neither startup activity nor the sentinel can race the listeners.
     const observed =
       observe && completionToken
         ? yield* observeTerminalCompletion({
@@ -391,25 +446,63 @@ export const make = Effect.gen(function* () {
             onOutputLine: observe.onOutputLine,
           })
         : undefined;
+    // PowerShell has no line-editor signal; keep its immediate write.
+    const readiness =
+      completionShell === "powershell"
+        ? undefined
+        : yield* watchShellReadiness({
+            threadId: input.threadId,
+            terminalId,
+            onStartupPrompt: observed?.flushPartialLine ?? Effect.void,
+          });
 
     yield* terminalManager
-      .write({
+      .open({
         threadId: input.threadId,
         terminalId,
-        data: projectScriptTerminalInput(commandLine),
+        cwd,
+        worktreePath: input.worktreePath,
+        env: { ...env, NO_COLOR: "1", FORCE_COLOR: "0" },
       })
       .pipe(
         Effect.mapError(
           (cause) =>
             new ProjectSetupScriptOperationError({
               ...errorContext,
-              operation: "writeCommand",
+              operation: "openTerminal",
               cause,
             }),
         ),
-        Effect.tapError(() => Effect.sync(() => observed?.unsubscribe())),
+        Effect.onError(() =>
+          Effect.sync(() => {
+            observed?.unsubscribe();
+            readiness?.unsubscribe();
+          }),
+        ),
       );
 
+    // Return once the terminal exists so callers can show it while a startup prompt waits.
+    yield* (readiness?.wait ?? Effect.succeed("ready" as const)).pipe(
+      Effect.flatMap((shell) =>
+        shell === "exited"
+          ? Effect.void
+          : terminalManager.write({
+              threadId: input.threadId,
+              terminalId,
+              data: projectScriptTerminalInput(commandLine),
+            }),
+      ),
+      Effect.catchCause((cause) =>
+        Effect.logWarning("project script command was not written", {
+          ...errorContext,
+          terminalId,
+          cause,
+        }).pipe(Effect.andThen(observed?.abandon ?? Effect.void)),
+      ),
+      Effect.ensuring(Effect.sync(() => readiness?.unsubscribe())),
+      Effect.forkIn(serviceScope),
+    );
+
     const completion = observed?.completion.pipe(
       Effect.tap(({ exitCode }) =>
         exitCode === 0