diff --git a/script/make-pretty b/script/make-pretty
index 9129ed81d..6df008405 100755
--- a/script/make-pretty
+++ b/script/make-pretty
@@ -133,7 +133,7 @@ do_shell_format()
     echo -e '     format shell'
     echo -e '====================='
 
-    shfmt -f . | grep -v -E "^($(echo "${OT_EXCLUDE_DIRS[@]}" | tr ' ' '|'))" \
+    git ls-files | xargs shfmt -f | grep -v -E "^($(echo "${OT_EXCLUDE_DIRS[@]}" | tr ' ' '|'))" \
         | xargs -n10 -P"$OT_BUILD_JOBS" shfmt -i 4 -bn -ci -fn -s -w
 }
 
@@ -143,10 +143,10 @@ do_shell_check()
     echo -e '     check shell'
     echo -e '====================='
 
-    shfmt -f . | grep -v -E "^($(echo "${OT_EXCLUDE_DIRS[@]}" | tr ' ' '|'))" \
+    git ls-files | xargs shfmt -f | grep -v -E "^($(echo "${OT_EXCLUDE_DIRS[@]}" | tr ' ' '|'))" \
         | xargs -n10 -P"$OT_BUILD_JOBS" shfmt -i 4 -bn -ci -fn -s -d
 
-    shfmt -f . | grep -v -E "^($(echo "${OT_EXCLUDE_DIRS[@]}" | tr ' ' '|'))" \
+    git ls-files | xargs shfmt -f | grep -v -E "^($(echo "${OT_EXCLUDE_DIRS[@]}" | tr ' ' '|'))" \
         | xargs -n10 -P"$OT_BUILD_JOBS" shellcheck
 }