diff --git a/shell/hooks/pre-commit.sh b/shell/hooks/pre-commit.sh
index 4ce4fa13..23776793 100755
--- a/shell/hooks/pre-commit.sh
+++ b/shell/hooks/pre-commit.sh
@@ -9,15 +9,25 @@ fi
 
 diff="git diff-index --name-only --cached $against --diff-filter d"
 
-all_files=($($diff))
+mapfile -t all_files < <($diff)
 
-# Format staged files.
+# Stash only unstaged changes, keeping staged changes
+old_stash=$(git rev-parse --quiet --verify refs/stash)
+git stash push --quiet --keep-index -m 'Unstaged changes before pre-commit hook'
+new_stash=$(git rev-parse --quiet --verify refs/stash)
+
+# Format staged files
 if ((${#all_files[@]} != 0)); then
   treefmt "${all_files[@]}" &&
     git add "${all_files[@]}"
 fi
 
-# check editorconfig
+# If unstaged changes were stashed re-apply to working tree
+if [ "$old_stash" != "$new_stash" ]; then
+  git stash pop --quiet
+fi
+
+# Check editorconfig
 if ((${#all_files[@]} != 0)); then
   if ! editorconfig-checker -- "${all_files[@]}"; then
     printf "%b\n" \