diff --git a/src/Chunk.ts b/src/Chunk.ts
index 11e6e3035dd..bb7fdee3484 100644
--- a/src/Chunk.ts
+++ b/src/Chunk.ts
@@ -464,7 +464,7 @@ export default class Chunk {
 			});
 			const currentPath = `${currentDir}/${fileName}`;
 			const { preserveModulesRoot } = options;
-			if (preserveModulesRoot && currentPath.startsWith(preserveModulesRoot)) {
+			if (preserveModulesRoot && resolve(currentPath).startsWith(preserveModulesRoot)) {
 				path = currentPath.slice(preserveModulesRoot.length).replace(/^[\\/]/, '');
 			} else {
 				path = relative(preserveModulesRelativeDir, currentPath);
diff --git a/test/chunking-form/samples/preserve-modules-root/_config.js b/test/chunking-form/samples/preserve-modules-root/_config.js
index 61ff285d344..5518c9c5483 100644
--- a/test/chunking-form/samples/preserve-modules-root/_config.js
+++ b/test/chunking-form/samples/preserve-modules-root/_config.js
@@ -7,6 +7,14 @@ module.exports = {
 	options: {
 		input: ['src/under-build.js', 'src/below/module.js'],
 		plugins: [
+			{
+				name: 'convert-slashes',
+				// This simulates converted slashes as used by e.g. Vite
+				async resolveId(source, importer, options) {
+					const resolved = await this.resolve(source, importer, { ...options, skipSelf: true });
+					return { ...resolved, id: resolved.id.replace(/\\/g, '/') };
+				}
+			},
 			resolve({
 				moduleDirectories: ['custom_modules']
 			}),