diff --git a/lib/worker/subprocess.js b/lib/worker/subprocess.js
index 4a31fdb32..90b829d6a 100644
--- a/lib/worker/subprocess.js
+++ b/lib/worker/subprocess.js
@@ -105,7 +105,6 @@ ipc.options.then(options => {
 
 	// Install before processing options.require, so if helpers are added to the
 	// require configuration the *compiled* helper will be loaded.
-	dependencyTracking.install(testPath);
 	precompilerHook.install();
 
 	try {
@@ -120,6 +119,10 @@ ipc.options.then(options => {
 			} catch (_) {}
 		}
 
+		// Install dependency tracker after the require configuration has been evaluated
+		// to make sure we also track dependencies with custom require hooks
+		dependencyTracking.install(testPath);
+
 		require(testPath);
 
 		if (accessedRunner) {
diff --git a/test/fixture/watcher/with-custom-ext-dependencies/ava.config.js b/test/fixture/watcher/with-custom-ext-dependencies/ava.config.js
new file mode 100644
index 000000000..f68647003
--- /dev/null
+++ b/test/fixture/watcher/with-custom-ext-dependencies/ava.config.js
@@ -0,0 +1,3 @@
+export default {
+	sources: ['source.custom-ext', 'setup.js']
+};
diff --git a/test/fixture/watcher/with-custom-ext-dependencies/package.json b/test/fixture/watcher/with-custom-ext-dependencies/package.json
new file mode 100644
index 000000000..0967ef424
--- /dev/null
+++ b/test/fixture/watcher/with-custom-ext-dependencies/package.json
@@ -0,0 +1 @@
+{}
diff --git a/test/fixture/watcher/with-custom-ext-dependencies/setup.js b/test/fixture/watcher/with-custom-ext-dependencies/setup.js
new file mode 100644
index 000000000..b53dd5153
--- /dev/null
+++ b/test/fixture/watcher/with-custom-ext-dependencies/setup.js
@@ -0,0 +1,9 @@
+'use strict';
+
+const fs = require('fs');
+
+// eslint-disable-next-line node/no-deprecated-api
+require.extensions['.custom-ext'] = function (module, filename) {
+	const content = fs.readFileSync(filename, 'utf8');
+	module._compile(content, filename);
+};
diff --git a/test/fixture/watcher/with-custom-ext-dependencies/source.custom-ext b/test/fixture/watcher/with-custom-ext-dependencies/source.custom-ext
new file mode 100644
index 000000000..80b9ab875
--- /dev/null
+++ b/test/fixture/watcher/with-custom-ext-dependencies/source.custom-ext
@@ -0,0 +1,2 @@
+'use strict';
+module.exports = true;
diff --git a/test/fixture/watcher/with-custom-ext-dependencies/test-1.js b/test/fixture/watcher/with-custom-ext-dependencies/test-1.js
new file mode 100644
index 000000000..fdc5398a8
--- /dev/null
+++ b/test/fixture/watcher/with-custom-ext-dependencies/test-1.js
@@ -0,0 +1,6 @@
+import test from '../../../..';
+import dependency from './source.custom-ext';
+
+test('works', t => {
+	t.truthy(dependency);
+});
diff --git a/test/fixture/watcher/with-custom-ext-dependencies/test-2.js b/test/fixture/watcher/with-custom-ext-dependencies/test-2.js
new file mode 100644
index 000000000..a7b86803a
--- /dev/null
+++ b/test/fixture/watcher/with-custom-ext-dependencies/test-2.js
@@ -0,0 +1,5 @@
+import test from '../../../..';
+
+test('works', t => {
+	t.pass();
+});
diff --git a/test/integration/watcher.js b/test/integration/watcher.js
index c501f3237..69a2adce9 100644
--- a/test/integration/watcher.js
+++ b/test/integration/watcher.js
@@ -82,6 +82,54 @@ test('watcher reruns test files when source dependencies change', t => {
 	});
 });
 
+test('watcher reruns ONLY test files that depend on a changed source with custom extension', t => {
+	let killed = false;
+
+	const child = execCli(['--verbose', '--require', './setup.js', '--watch', 'test-1.js', 'test-2.js'], {dirname: 'fixture/watcher/with-custom-ext-dependencies', env: {CI: ''}}, err => {
+		t.ok(killed);
+		t.ifError(err);
+		t.end();
+	});
+
+	let buffer = '';
+	let passedFirst = false;
+	child.stdout.on('data', str => {
+		buffer += str;
+		if (buffer.includes('2 tests passed') && !passedFirst) {
+			touch.sync(path.join(__dirname, '../fixture/watcher/with-custom-ext-dependencies/source.custom-ext'));
+			buffer = '';
+			passedFirst = true;
+		} else if (buffer.includes('1 test passed') && !killed) {
+			child.kill();
+			killed = true;
+		}
+	});
+});
+
+test('watcher reruns all tests when one of the configured files in the `require` option changes', t => {
+	let killed = false;
+
+	const child = execCli(['--verbose', '--require', './setup.js', '--watch', 'test-1.js', 'test-2.js'], {dirname: 'fixture/watcher/with-custom-ext-dependencies', env: {CI: ''}}, err => {
+		t.ok(killed);
+		t.ifError(err);
+		t.end();
+	});
+
+	let buffer = '';
+	let passedFirst = false;
+	child.stdout.on('data', str => {
+		buffer += str;
+		if (buffer.includes('2 tests passed') && !passedFirst) {
+			touch.sync(path.join(__dirname, '../fixture/watcher/with-custom-ext-dependencies/setup.js'));
+			buffer = '';
+			passedFirst = true;
+		} else if (buffer.includes('2 tests passed') && !killed) {
+			child.kill();
+			killed = true;
+		}
+	});
+});
+
 test('watcher does not rerun test files when they write snapshot files', t => {
 	let killed = false;