diff --git a/packages/run/src/index.ts b/packages/run/src/index.ts
index afeda6862..39f6806a0 100644
--- a/packages/run/src/index.ts
+++ b/packages/run/src/index.ts
@@ -16,7 +16,7 @@ export default function run(opts: RollupRunOptions = {}): Plugin {
   return {
     name: 'run',
 
-    options(options) {
+    buildStart(options) {
       let inputs = options.input!;
 
       if (typeof inputs === 'string') {
@@ -32,7 +32,6 @@ export default function run(opts: RollupRunOptions = {}): Plugin {
       }
 
       input = path.resolve(inputs[0]);
-      return options;
     },
 
     generateBundle(_outputOptions, _bundle, isWrite) {
@@ -43,23 +42,14 @@ export default function run(opts: RollupRunOptions = {}): Plugin {
 
     writeBundle(outputOptions, bundle) {
       const dir = outputOptions.dir || path.dirname(outputOptions.file!);
-
-      let dest: string | undefined;
-      for (const fileName of Object.keys(bundle)) {
+      const entryFileName = Object.keys(bundle).find((fileName) => {
         const chunk = bundle[fileName] as RenderedChunk;
+        return chunk.isEntry && chunk.facadeModuleId === input;
+      });
 
-        // eslint-disable-next-line no-continue
-        if (!chunk.isEntry) continue;
-
-        if (chunk.isEntry && chunk.modules[input]) {
-          dest = path.join(dir, fileName);
-          break;
-        }
-      }
-
-      if (dest) {
+      if (entryFileName) {
         if (proc) proc.kill();
-        proc = fork(dest, args, forkOptions);
+        proc = fork(path.join(dir, entryFileName), args, forkOptions);
       } else {
         this.error(`@rollup/plugin-run could not find output chunk`);
       }
diff --git a/packages/run/test/fixtures/facade-entry/dynamic.js b/packages/run/test/fixtures/facade-entry/dynamic.js
new file mode 100644
index 000000000..6c82d092b
--- /dev/null
+++ b/packages/run/test/fixtures/facade-entry/dynamic.js
@@ -0,0 +1,3 @@
+import log from './library';
+
+log(0);
diff --git a/packages/run/test/fixtures/facade-entry/index.js b/packages/run/test/fixtures/facade-entry/index.js
new file mode 100644
index 000000000..a2002c175
--- /dev/null
+++ b/packages/run/test/fixtures/facade-entry/index.js
@@ -0,0 +1,6 @@
+import log from './library';
+
+log(0);
+(async () => {
+  await import('./dynamic');
+})();
diff --git a/packages/run/test/fixtures/facade-entry/library.js b/packages/run/test/fixtures/facade-entry/library.js
new file mode 100644
index 000000000..b92fec258
--- /dev/null
+++ b/packages/run/test/fixtures/facade-entry/library.js
@@ -0,0 +1,2 @@
+const log = (value) => console.log(value);
+export default log;
diff --git a/packages/run/test/test.js b/packages/run/test/test.js
index c8a53e68b..99e76a190 100644
--- a/packages/run/test/test.js
+++ b/packages/run/test/test.js
@@ -38,6 +38,33 @@ test('builds the bundle and forks a child process', async (t) => {
   t.true(mockChildProcess.calledWithExactly(outputOptions.file, [], {}));
 });
 
+test('takes input from the latest options', async (t) => {
+  const bundle = await rollup({
+    input: 'incorrect',
+    plugins: [
+      run(),
+      {
+        options(options) {
+          options.input = input;
+          return options;
+        }
+      }
+    ]
+  });
+  await bundle.write(outputOptions);
+  t.true(mockChildProcess.calledWithExactly(outputOptions.file, [], {}));
+});
+
+test('checks entry point facade module', async (t) => {
+  const bundle = await rollup({
+    input: join(cwd, 'facade-entry/index.js'),
+    plugins: [run()]
+  });
+  const outputDir = join(cwd, 'output');
+  await bundle.write({ dir: outputDir, format: 'cjs' });
+  t.true(mockChildProcess.calledWithExactly(join(outputDir, 'index.js'), [], {}));
+});
+
 test('allows pass-through options for child_process.fork', async (t) => {
   const forkOptions = {
     cwd,
@@ -48,7 +75,6 @@ test('allows pass-through options for child_process.fork', async (t) => {
     input,
     plugins: [run(forkOptions)]
   });
-
   await bundle.write(outputOptions);
   t.true(mockChildProcess.calledWithExactly(outputOptions.file, [], forkOptions));
 });