diff --git a/src/runtime/test_runner/Execution.rs b/src/runtime/test_runner/Execution.rs
index eaa66cf9f051..4c5760b6382c 100644
--- a/src/runtime/test_runner/Execution.rs
+++ b/src/runtime/test_runner/Execution.rs
@@ -570,7 +570,11 @@ impl Execution {
 
     fn on_group_completed(global_this: &JSGlobalObject) {
         // SAFETY: bun_vm() returns the live per-thread VM.
-        global_this.bun_vm().as_mut().auto_killer.disable();
+        let vm = global_this.bun_vm().as_mut();
+        // Under --isolate the swap between files kills and clears the tracked set.
+        if !vm.test_isolation_enabled {
+            vm.auto_killer.disable();
+        }
     }
 
     fn on_sequence_started(sequence: &mut ExecutionSequence) {
diff --git a/test/cli/test/isolation.test.ts b/test/cli/test/isolation.test.ts
index 2f052f268f16..5d011b966c87 100644
--- a/test/cli/test/isolation.test.ts
+++ b/test/cli/test/isolation.test.ts
@@ -2,6 +2,7 @@ import { describe, expect, setDefaultTimeout, test } from "bun:test";
 import { bunEnv, bunExe, isASAN, normalizeBunSnapshot, tempDir } from "harness";
 import fs from "node:fs";
 import net from "node:net";
+import { join } from "node:path";
 
 // Every case spawns at least one full `bun test --isolate` child; the heavy
 // ones (8-file leak fixtures, 500-2000-export module_info modules) exceed the
@@ -411,6 +412,67 @@ describe.concurrent("bun test --isolate", () => {
     expect(normalizeBunSnapshot(stderr, dir)).toContain("0 fail");
     expect(exitCode).toBe(0);
   });
+
+  // Every file spawns a sleeper at module scope (outside any test or hook),
+  // appends its pid to a shared log, and its test asserts that the sleepers
+  // logged by the files that ran before it are gone. The first file's sleeper
+  // is always killed; the third file is what proves the second file's
+  // module-scope sleeper was killed at its isolation swap too. Holds in any
+  // file order, so the same fixture covers a --parallel worker running
+  // several files.
+  const moduleScopeSpawnFile = `
+    import { test, expect } from "bun:test";
+    import fs from "node:fs";
+    const log = process.env.PID_LOG!;
+    const earlier = fs.readFileSync(log, "utf8").split("\\n").filter(Boolean).map(Number);
+    const child = Bun.spawn({ cmd: [process.execPath, "-e", "setInterval(()=>{}, 1e6)"], stdout: "ignore", stderr: "ignore" });
+    fs.appendFileSync(log, child.pid + "\\n");
+    const isAlive = (pid: number) => { try { process.kill(pid, 0); return true; } catch { return false; } };
+    test("module-scope sleepers of the files before this one were killed", async () => {
+      // The swap sends SIGTERM; the sleeper may still be getting reaped.
+      const deadline = Date.now() + 2_000;
+      while (earlier.some(isAlive) && Date.now() < deadline) await Bun.sleep(10);
+      expect(earlier.filter(isAlive)).toEqual([]);
+    });
+  `;
+
+  test.each([
+    ["--isolate", ["--isolate"], {}],
+    // One worker takes all three files (scale-up gated), so the worker's
+    // per-file swap is what has to kill the second and third sleepers.
+    ["--parallel worker", ["--parallel=2"], { BUN_TEST_PARALLEL_SCALE_MS: "60000" }],
+  ])("module-scope subprocesses are killed for every isolated file, not just the first (%s)", async (_, args, env) => {
+    using dir = tempDir("isolate-module-scope-subprocess", {
+      "a.test.ts": moduleScopeSpawnFile,
+      "b.test.ts": moduleScopeSpawnFile,
+      "c.test.ts": moduleScopeSpawnFile,
+      "pids.txt": "",
+    });
+    const log = join(String(dir), "pids.txt");
+    const loggedPids = () => fs.readFileSync(log, "utf8").split("\n").filter(Boolean);
+    try {
+      await using proc = Bun.spawn({
+        cmd: [bunExe(), "test", ...args, "./a.test.ts", "./b.test.ts", "./c.test.ts"],
+        env: { ...bunEnv, ...env, PID_LOG: log },
+        cwd: String(dir),
+        stderr: "pipe",
+        stdout: "pipe",
+      });
+      const [, stderr, exitCode] = await Promise.all([proc.stdout.text(), proc.stderr.text(), proc.exited]);
+      expect(normalizeBunSnapshot(stderr, dir)).toContain("3 pass");
+      expect(normalizeBunSnapshot(stderr, dir)).toContain("0 fail");
+      expect(loggedPids()).toHaveLength(3);
+      expect(exitCode).toBe(0);
+    } finally {
+      // Nothing swaps after the last file of a serial run, so its sleeper is
+      // ours to kill, as is anything an unfixed runner leaked.
+      for (const pid of loggedPids()) {
+        try {
+          process.kill(Number(pid));
+        } catch {}
+      }
+    }
+  });
 });
 
 // The eviction test below proves the SourceProvider cache is active (control: