diff --git a/color-tool b/color-tool
index 8c7db5a..a74cbd4 100755
--- a/color-tool
+++ b/color-tool
@@ -194,7 +194,33 @@ set_config() {
       
       if [[ -n "$new_val" ]]; then
         if [[ "$original_line" =~ ^([[:space:]]*[A-Za-z_]+[[:space:]]*=[[:space:]]*)([^[:space:]#]+)(.*)$ ]]; then
-           echo "${BASH_REMATCH[1]}$new_val${BASH_REMATCH[3]}" >> "$temp_file"
+           local prefix="${BASH_REMATCH[1]}"
+           local old_val="${BASH_REMATCH[2]}"
+           local suffix="${BASH_REMATCH[3]}"
+           
+           # Adjust whitespace to keep comments aligned if the value length changed
+           if [[ "$key" != "output" ]]; then
+             local old_len=${#old_val}
+             local new_len=${#new_val}
+             local diff=$((old_len - new_len))
+             
+             if [[ $diff -gt 0 ]]; then
+               # new value is shorter, add spaces to suffix
+               local spaces=""
+               for ((i=0; i<diff; i++)); do spaces+=" "; done
+               suffix="$spaces$suffix"
+             elif [[ $diff -lt 0 ]]; then
+               # new value is longer, remove spaces from suffix
+               local remove=$((-diff))
+               for ((i=0; i<remove; i++)); do
+                 if [[ "$suffix" == " "* ]]; then
+                   suffix="${suffix# }"
+                 fi
+               done
+             fi
+           fi
+           
+           echo "$prefix$new_val$suffix" >> "$temp_file"
            continue
         elif [[ "$original_line" =~ ^([[:space:]]*[A-Za-z_]+[[:space:]]*=[[:space:]]*)(.*)$ ]]; then
            echo "${BASH_REMATCH[1]}$new_val" >> "$temp_file"