diff --git a/CHANGELOG.md b/CHANGELOG.md
index 16262bd1c3..a5795245a2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@
 - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
 - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991))
 - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
+- return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 8c50f0a49f..1a1e8a2a99 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -1069,7 +1069,7 @@ def determine_base_dir(directory="."):
         config_fn = get_first_available_path(base_dir, CONFIG_PATHS)
         if config_fn:
             break
-    return directory if base_dir == start_dir else base_dir
+    return directory if (base_dir == start_dir or str(base_dir) == base_dir.root) else base_dir
 
 
 def get_first_available_path(directory, paths):