diff --git a/src/core/create_manifests.ts b/src/core/create_manifests.ts
index 4c0b2a9..1e1a09a 100644
--- a/src/core/create_manifests.ts
+++ b/src/core/create_manifests.ts
@@ -204,9 +204,12 @@ function generate_server(
 			error
 		};`.replace(/^\t\t/gm, '').trim();
 
+	const build_dir = path.relative(process.cwd(), locations.dest());
+	const src_dir = path.relative(process.cwd(), locations.src());
+
 	return `// This file is generated by Sapper — do not edit it!\n` + template
-		.replace('__BUILD__DIR__', JSON.stringify(locations.dest()))
-		.replace('__SRC__DIR__', JSON.stringify(locations.src()))
+		.replace('__BUILD__DIR__', JSON.stringify(build_dir))
+		.replace('__SRC__DIR__', JSON.stringify(src_dir))
 		.replace('__DEV__', dev() ? 'true' : 'false')
 		.replace(/const manifest = __MANIFEST__;/, code);
 }