diff --git a/emap-setup/emap_runner/runner.py b/emap-setup/emap_runner/runner.py
index 04317aef0..67914a7f2 100644
--- a/emap-setup/emap_runner/runner.py
+++ b/emap-setup/emap_runner/runner.py
@@ -157,7 +157,6 @@ def setup(self) -> None:
         repos = self.global_config.extract_repositories(branch_name=self.args.branch)
 
         if self.args.init:
-            repos.clean(print_warnings=False)
             repos.clone()
 
         elif self.args.update: