diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6fb6955ecb..2e583e606b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@
 ### General
 
 - Fix error in tagging GitPod docker images during releases
+- Don't remove local copy of modules repo, only update it with fetch ([#1879](https://github.com/nf-core/tools/pull/1879))
 
 ### Modules
 
diff --git a/nf_core/modules/modules_command.py b/nf_core/modules/modules_command.py
index 116cd1287e..1020158b78 100644
--- a/nf_core/modules/modules_command.py
+++ b/nf_core/modules/modules_command.py
@@ -169,8 +169,7 @@ def check_modules_structure(self):
             if len(wrong_location_modules) > 0:
                 log.info("The modules folder structure is outdated. Reinstalling modules.")
                 # Remove the local copy of the modules repository
-                log.info(f"Removing '{self.modules_repo.local_repo_dir}'")
-                shutil.rmtree(self.modules_repo.local_repo_dir)
+                log.info(f"Updating '{self.modules_repo.local_repo_dir}'")
                 self.modules_repo.setup_local_repo(
                     self.modules_repo.remote_url, self.modules_repo.branch, self.hide_progress
                 )