diff --git a/apps/server/src/project/ProjectSetupScriptRunner.test.ts b/apps/server/src/project/ProjectSetupScriptRunner.test.ts
index 69c553a4deaf..52f57165ba58 100644
--- a/apps/server/src/project/ProjectSetupScriptRunner.test.ts
+++ b/apps/server/src/project/ProjectSetupScriptRunner.test.ts
@@ -149,6 +149,75 @@ describe("ProjectSetupScriptRunner", () => {
     );
   });
 
+  it.effect("gives a multi-repo cousin its own terminal and its original repo root", () => {
+    const open = vi.fn(() =>
+      Effect.succeed({
+        threadId: "thread-1",
+        terminalId: "setup-default-setup-web",
+        cwd: "/repo/worktrees/t/web",
+        worktreePath: "/repo/worktrees/t/web",
+        status: "running" as const,
+        pid: 123,
+        history: "",
+        exitCode: null,
+        exitSignal: null,
+        label: "setup-default-setup-web",
+        updatedAt: "2026-01-01T00:00:00.000Z",
+      }),
+    );
+    return Effect.gen(function* () {
+      const runner = yield* ProjectSetupScriptRunner.ProjectSetupScriptRunner;
+      yield* runner.runForThread({
+        threadId: "thread-1",
+        projectId: "project-1",
+        worktreePath: "/repo/worktrees/t/web",
+        repoRoot: "/repo/web",
+        terminalIdSuffix: "web",
+      });
+      expect(open).toHaveBeenCalledWith({
+        threadId: "thread-1",
+        terminalId: "setup-default-setup-web",
+        cwd: "/repo/worktrees/t/web",
+        worktreePath: "/repo/worktrees/t/web",
+        env: {
+          T3CODE_PROJECT_ROOT: "/repo/project",
+          T3CODE_WORKTREE_PATH: "/repo/worktrees/t/web",
+          T3CODE_REPO_ROOT: "/repo/web",
+          NO_COLOR: "1",
+          FORCE_COLOR: "0",
+        },
+      });
+    }).pipe(
+      Effect.provide(
+        testLayer(
+          makeProject([]),
+          { open, write: () => Effect.void },
+          ServerSettings.layerTest({
+            defaultProjectScripts: [
+              {
+                id: "default-setup",
+                name: "Setup",
+                command: "npm install",
+                icon: "configure",
+                runOnWorktreeCreate: true,
+              },
+            ],
+          }),
+        ),
+      ),
+    );
+  });
+
+  it("keeps long setup terminal ids distinct within the terminal id limit", () => {
+    const repoPrefix = "service-".repeat(20);
+    const api = ProjectSetupScriptRunner.setupTerminalId("setup", `${repoPrefix}api`);
+    const web = ProjectSetupScriptRunner.setupTerminalId("setup", `${repoPrefix}web`);
+    expect(api).not.toBe(web);
+    expect(api.length).toBeLessThanOrEqual(128);
+    expect(web.length).toBeLessThanOrEqual(128);
+    expect(ProjectSetupScriptRunner.setupTerminalId("setup", "web")).toBe("setup-setup-web");
+  });
+
   it.effect("returns no-script when no setup script exists", () => {
     const open = vi.fn(() => Effect.die("unexpected open"));
     const write = vi.fn(() => Effect.die("unexpected write"));
diff --git a/apps/server/src/project/ProjectSetupScriptRunner.ts b/apps/server/src/project/ProjectSetupScriptRunner.ts
index 738440c8531d..c171e43883d6 100644
--- a/apps/server/src/project/ProjectSetupScriptRunner.ts
+++ b/apps/server/src/project/ProjectSetupScriptRunner.ts
@@ -199,6 +199,20 @@ function wrapCommandForCompletion(
   }
 }
 
+const TERMINAL_ID_MAX_LENGTH = 128;
+
+/**
+ * The setup terminal's id. Ids over the terminal limit keep a hash of the full
+ * id, so two repos whose suffixes differ only past the limit still get their
+ * own terminal instead of one stopping the other's script.
+ */
+export function setupTerminalId(scriptId: string, suffix?: string): string {
+  const id = suffix ? `setup-${scriptId}-${suffix}` : `setup-${scriptId}`;
+  if (id.length <= TERMINAL_ID_MAX_LENGTH) return id;
+  const hash = NodeCrypto.createHash("sha256").update(id).digest("hex").slice(0, 12);
+  return `${id.slice(0, TERMINAL_ID_MAX_LENGTH - hash.length - 1)}-${hash}`;
+}
+
 /** @public Service construction is part of the canonical Effect module API. */
 export const make = Effect.gen(function* () {
   const projectionSnapshotQuery = yield* ProjectionSnapshotQuery.ProjectionSnapshotQuery;
@@ -354,10 +368,7 @@ export const make = Effect.gen(function* () {
     }
 
     const terminalId =
-      input.preferredTerminalId ??
-      (input.terminalIdSuffix
-        ? `setup-${script.id}-${input.terminalIdSuffix}`.slice(0, 128)
-        : `setup-${script.id}`);
+      input.preferredTerminalId ?? setupTerminalId(script.id, input.terminalIdSuffix);
     const cwd = input.worktreePath;
     const env = projectScriptRuntimeEnv({
       project: { cwd: project.workspaceRoot },