diff --git a/src/runtime/jsc_hooks.rs b/src/runtime/jsc_hooks.rs
index bdd8ac7f48f8..cad7564a5787 100644
--- a/src/runtime/jsc_hooks.rs
+++ b/src/runtime/jsc_hooks.rs
@@ -2845,6 +2845,13 @@ fn transpile_source_code_inner(
                     return Err(crate::Error::ParseError);
                 }
 
+                // Set before the early returns below (cache hit, `// @bun`, async queue):
+                // every later module load is gated on this flag.
+                if is_main && !disable_transpilying {
+                    // SAFETY: per fn contract — `jsc_vm` is the live per-thread VM.
+                    unsafe { (*jsc_vm).has_loaded = true };
+                }
+
                 let source = &parse_result.source;
 
                 // Raw JSON: hand the source bytes straight to JSC.
@@ -3269,11 +3276,6 @@ fn transpile_source_code_inner(
                     print_result?;
                 }
 
-                if is_main {
-                    // SAFETY: per fn contract — `jsc_vm` is the live per-thread VM.
-                    unsafe { (*jsc_vm).has_loaded = true };
-                }
-
                 // `module_info.asDeserialized()`: finalize the
                 // printer-filled record into the FFI shape consumed by C++
                 // (freed by C++ `~SourceProvider` via
diff --git a/test/cli/run/run-cjs.test.ts b/test/cli/run/run-cjs.test.ts
index ebf49dba3f5a..6c214dd6111b 100644
--- a/test/cli/run/run-cjs.test.ts
+++ b/test/cli/run/run-cjs.test.ts
@@ -1,6 +1,6 @@
 import { describe, expect, test } from "bun:test";
 import { mkdirSync } from "fs";
-import { bunEnv, bunExe, tmpdirSync } from "harness";
+import { bunEnv, bunExe, tempDir, tmpdirSync } from "harness";
 import { join } from "path";
 
 describe.concurrent("run-cjs", () => {
@@ -17,4 +17,31 @@ describe.concurrent("run-cjs", () => {
     const stdout = await proc.stdout.text();
     expect(stdout).toEqual("hello world\n");
   });
+
+  test("a pre-bundled entry point still consults require.extensions", async () => {
+    // `bun build --target=bun --format=cjs` emits this header, and the `// @bun`
+    // pragma makes the parser hand the source straight to JSC without printing
+    // it. That must not change how the modules this entry loads are resolved.
+    using dir = tempDir("run-cjs-bundled-entry", {
+      "entry.cjs": `// @bun @bun-cjs
+(function(exports, require, module, __filename, __dirname) {
+  require.extensions[".data"] = (module, filename) => {
+    module.exports = "custom-loader";
+  };
+  console.log(require("./asset.data"));
+})`,
+      // If the custom loader is skipped, this is transpiled as JS/TS instead.
+      "asset.data": `module.exports = "default-loader";`,
+    });
+
+    await using proc = Bun.spawn({
+      cmd: [bunExe(), "entry.cjs"],
+      cwd: String(dir),
+      env: bunEnv,
+      stdout: "pipe",
+      stderr: "pipe",
+    });
+    const [stdout, stderr, exitCode] = await Promise.all([proc.stdout.text(), proc.stderr.text(), proc.exited]);
+    expect({ stdout, stderr, exitCode }).toMatchObject({ stdout: "custom-loader\n", exitCode: 0 });
+  });
 });
diff --git a/test/cli/run/transpiler-cache.test.ts b/test/cli/run/transpiler-cache.test.ts
index 2b6561b37bb2..01d569bb15ab 100644
--- a/test/cli/run/transpiler-cache.test.ts
+++ b/test/cli/run/transpiler-cache.test.ts
@@ -249,6 +249,49 @@ describe("transpiler cache", () => {
     expect(run(["--feature=OTHER", "--feature=SUPER_SECRET"])).toBe("enabled");
     expect(newCacheCount()).toBe(0); // cache hit, order doesn't matter
   });
+
+  // Serving the entry point from the cache must not change how the modules it
+  // loads are resolved. Both of these are gated on the `has_loaded` flag, which
+  // used to be set only on the path that runs the printer.
+  describe("a cached entry point does not change how later modules load", () => {
+    // Padding so the entry point clears MINIMUM_CACHE_SIZE (4 KiB) and is
+    // eligible for the cache at all.
+    const filler = "\n//" + Buffer.alloc(5 * 1024, "f").toString();
+
+    test("require.extensions is still consulted", async () => {
+      writeFileSync(
+        join(temp_dir, "entry.js"),
+        `require.extensions[".data"] = (module, filename) => {
+           module.exports = "custom-loader";
+         };
+         console.log(require("./asset.data"));${filler}`,
+      );
+      // If the custom loader is skipped, this is transpiled as JS/TS instead.
+      writeFileSync(join(temp_dir, "asset.data"), `module.exports = "default-loader";`);
+
+      expect(await bunRun(join(temp_dir, "entry.js"), env)).toSpawn("custom-loader");
+      expect(newCacheCount()).toBe(1);
+
+      expect(await bunRun(join(temp_dir, "entry.js"), env)).toSpawn("custom-loader");
+      expect(newCacheCount()).toBe(0);
+    });
+
+    test("unknown extensions still use the file loader", async () => {
+      writeFileSync(
+        join(temp_dir, "entry.mjs"),
+        `import asset from "./asset.someext";
+         console.log(typeof asset === "string" ? "file-loader" : "???");${filler}`,
+      );
+      // Not valid JS/TS, so a non-file loader fails the run outright.
+      writeFileSync(join(temp_dir, "asset.someext"), `hello world contents\n`);
+
+      expect(await bunRun(join(temp_dir, "entry.mjs"), env)).toSpawn("file-loader");
+      expect(newCacheCount()).toBe(1);
+
+      expect(await bunRun(join(temp_dir, "entry.mjs"), env)).toSpawn("file-loader");
+      expect(newCacheCount()).toBe(0);
+    });
+  });
 });
 
 test("rejects cached module records containing out-of-range string indices", () => {