diff --git a/test/cli/samples/wait-for-bundle-input-object/_config.js b/test/cli/samples/wait-for-bundle-input-object/_config.js
index 981f3ba47a9..4bda6e35d5c 100644
--- a/test/cli/samples/wait-for-bundle-input-object/_config.js
+++ b/test/cli/samples/wait-for-bundle-input-object/_config.js
@@ -1,5 +1,6 @@
 const fs = require('fs');
 const path = require('path');
+const { atomicWriteFileSync } = require('../../../utils');
 
 let second;
 let third;
@@ -17,9 +18,9 @@ module.exports = {
 	},
 	abortOnStderr(data) {
 		if (data.includes('waiting for input second')) {
-			fs.writeFileSync(second, "export default 'second'");
+			atomicWriteFileSync(second, "export default 'second'");
 		} else if (data.includes('waiting for input third')) {
-			fs.writeFileSync(third, "export default 'third'");
+			atomicWriteFileSync(third, "export default 'third'");
 		}
 	}
 };
diff --git a/test/cli/samples/wait-for-bundle-input/_config.js b/test/cli/samples/wait-for-bundle-input/_config.js
index 045097c443b..64f197395b4 100644
--- a/test/cli/samples/wait-for-bundle-input/_config.js
+++ b/test/cli/samples/wait-for-bundle-input/_config.js
@@ -1,5 +1,6 @@
 const fs = require('fs');
 const path = require('path');
+const { atomicWriteFileSync } = require('../../../utils');
 
 let mainFile;
 
@@ -15,7 +16,7 @@ module.exports = {
 	abortOnStderr(data) {
 		if (data.includes('waiting for input main.js')) {
 			// wait longer than one polling interval
-			setTimeout(() => fs.writeFileSync(mainFile, 'export default 42;'), 600);
+			setTimeout(() => atomicWriteFileSync(mainFile, 'export default 42;'), 600);
 		}
 	}
 };
diff --git a/test/cli/samples/watch/bundle-error/_config.js b/test/cli/samples/watch/bundle-error/_config.js
index 7b101a1bc14..2f38a2e2407 100644
--- a/test/cli/samples/watch/bundle-error/_config.js
+++ b/test/cli/samples/watch/bundle-error/_config.js
@@ -1,5 +1,6 @@
 const fs = require('fs');
 const path = require('path');
+const { atomicWriteFileSync } = require('../../../../utils');
 
 let mainFile;
 
@@ -16,7 +17,7 @@ module.exports = {
 	},
 	abortOnStderr(data) {
 		if (data.includes('Error: Unexpected token')) {
-			setTimeout(() => fs.writeFileSync(mainFile, 'export default 42;'), 500);
+			setTimeout(() => atomicWriteFileSync(mainFile, 'export default 42;'), 500);
 			return false;
 		}
 		if (data.includes('created _actual')) {
diff --git a/test/cli/samples/watch/watch-config-early-update/_config.js b/test/cli/samples/watch/watch-config-early-update/_config.js
index c13c2690ab6..cd26f5c990c 100644
--- a/test/cli/samples/watch/watch-config-early-update/_config.js
+++ b/test/cli/samples/watch/watch-config-early-update/_config.js
@@ -1,5 +1,6 @@
 const fs = require('fs');
 const path = require('path');
+const { atomicWriteFileSync } = require('../../../../utils');
 
 let configFile;
 
@@ -34,7 +35,7 @@ module.exports = {
 	},
 	abortOnStderr(data) {
 		if (data === 'initial\n') {
-			fs.writeFileSync(
+			atomicWriteFileSync.writeFileSync(
 				configFile,
 				`
 				console.error('updated');
diff --git a/test/cli/samples/watch/watch-config-error/_config.js b/test/cli/samples/watch/watch-config-error/_config.js
index caa161f4052..149901b3e4e 100644
--- a/test/cli/samples/watch/watch-config-error/_config.js
+++ b/test/cli/samples/watch/watch-config-error/_config.js
@@ -1,5 +1,6 @@
 const fs = require('fs');
 const path = require('path');
+const { atomicWriteFileSync } = require('../../../../utils');
 
 let configFile;
 
@@ -25,12 +26,12 @@ module.exports = {
 	},
 	abortOnStderr(data) {
 		if (data.includes(`created _actual${path.sep}main1.js`)) {
-			fs.writeFileSync(configFile, 'throw new Error("Config contains errors");');
+			atomicWriteFileSync(configFile, 'throw new Error("Config contains errors");');
 			return false;
 		}
 		if (data.includes('Config contains errors')) {
 			setTimeout(() => {
-				fs.writeFileSync(
+				atomicWriteFileSync(
 					configFile,
 					'export default {\n' +
 						'\tinput: "main.js",\n' +
diff --git a/test/cli/samples/watch/watch-config-initial-error/_config.js b/test/cli/samples/watch/watch-config-initial-error/_config.js
index 9fd2eb4def9..d2ecd6532ec 100644
--- a/test/cli/samples/watch/watch-config-initial-error/_config.js
+++ b/test/cli/samples/watch/watch-config-initial-error/_config.js
@@ -1,5 +1,6 @@
 const fs = require('fs');
 const path = require('path');
+const { atomicWriteFileSync } = require('../../../../utils');
 
 let configFile;
 
@@ -16,7 +17,7 @@ module.exports = {
 	async abortOnStderr(data) {
 		if (data.includes('Config contains initial errors')) {
 			await new Promise(resolve => setTimeout(resolve, 100));
-			fs.writeFileSync(
+			atomicWriteFileSync(
 				configFile,
 				'export default {\n' +
 					'\tinput: "main.js",\n' +
diff --git a/test/cli/samples/watch/watch-config-no-update/_config.js b/test/cli/samples/watch/watch-config-no-update/_config.js
index 635d77d42d9..7bc29a79ab1 100644
--- a/test/cli/samples/watch/watch-config-no-update/_config.js
+++ b/test/cli/samples/watch/watch-config-no-update/_config.js
@@ -1,5 +1,6 @@
 const fs = require('fs');
 const path = require('path');
+const { atomicWriteFileSync } = require('../../../../utils');
 
 let configFile;
 const configContent =
@@ -23,7 +24,7 @@ module.exports = {
 	},
 	abortOnStderr(data) {
 		if (data.includes('created _actual/main.js')) {
-			fs.writeFileSync(configFile, configContent);
+			atomicWriteFileSync(configFile, configContent);
 			return new Promise(resolve => setTimeout(() => resolve(true), 500));
 		}
 	},
diff --git a/test/utils.js b/test/utils.js
index beb2c60d97b..23aecff9d3a 100644
--- a/test/utils.js
+++ b/test/utils.js
@@ -1,4 +1,5 @@
 const assert = require('assert');
+const fs = require('fs');
 const path = require('path');
 const fixturify = require('fixturify');
 const sander = require('sander');
@@ -14,6 +15,7 @@ exports.runTestSuiteWithSamples = runTestSuiteWithSamples;
 exports.assertDirectoriesAreEqual = assertDirectoriesAreEqual;
 exports.assertFilesAreEqual = assertFilesAreEqual;
 exports.assertIncludes = assertIncludes;
+exports.atomicWriteFileSync = atomicWriteFileSync;
 
 function normaliseError(error) {
 	delete error.stack;
@@ -220,3 +222,12 @@ function assertIncludes(actual, expected) {
 		throw err;
 	}
 }
+
+// Workaround a race condition in fs.writeFileSync that temporarily creates
+// an empty file for a brief moment which may be read by rollup watch - even
+// if the content being overwritten is identical.
+function atomicWriteFileSync(filePath, contents) {
+	const stagingPath = filePath + '_';
+	fs.writeFileSync(stagingPath, contents);
+	fs.renameSync(stagingPath, filePath);
+}