diff --git a/cli/src/commands/onboard.ts b/cli/src/commands/onboard.ts
index d890efba..41473d52 100644
--- a/cli/src/commands/onboard.ts
+++ b/cli/src/commands/onboard.ts
@@ -644,7 +644,18 @@ export async function onboard(opts: OnboardOptions): Promise<void> {
     const { runCommand } = await import("./run.js");
     // [nexus] Start bootstrap concurrently — health-check poll waits for server readiness
     const serverUrl = `http://${server.host}:${server.port}`;
-    const rootDir = process.cwd();
+    // [nexus] Prompt for project root directory (mirrors UI wizard flow)
+    let rootDir = process.cwd();
+    if (process.stdin.isTTY && process.stdout.isTTY) {
+      const answer = await p.text({
+        message: "Project root directory:",
+        initialValue: process.cwd(),
+        placeholder: process.cwd(),
+      });
+      if (!p.isCancel(answer) && answer) {
+        rootDir = answer;
+      }
+    }
     bootstrapNexusAgents(serverUrl, rootDir).catch((err: unknown) => {
       // [nexus] Bootstrap failures are non-fatal
       console.warn("[nexus] Agent bootstrap error:", err instanceof Error ? err.message : String(err));