diff --git a/src/bootstrap/src/core/config/config.rs b/src/bootstrap/src/core/config/config.rs
index b06147055f2a7..ebdcc999f664c 100644
--- a/src/bootstrap/src/core/config/config.rs
+++ b/src/bootstrap/src/core/config/config.rs
@@ -1314,7 +1314,13 @@ impl Config {
 
         // Set flags.
         config.paths = std::mem::take(&mut flags.paths);
-        config.skip = flags.skip.into_iter().chain(flags.exclude).collect();
+        config.skip = flags
+            .skip
+            .into_iter()
+            .chain(flags.exclude)
+            .map(|p| t!(config.src.join(p).canonicalize()))
+            .collect();
+
         config.include_default_paths = flags.include_default_paths;
         config.rustc_error_format = flags.rustc_error_format;
         config.json_output = flags.json_output;