You betcha! The only thing to note – it’s not a 1:1 switch so you’ll have to do a tiny bit of adjusting. (If you just replace your all purpose flour with the exact amount of whole wheat flour, your muffins might turn out a little too dense!)  Some bakers like to use half and half (half whole wheat + half all purpose), but you can also try using ⅓ of the amount of flour the recipe needs. E.g. If it calls for 1 cup of all purpose flour, try only using ⅓ cup of whole wheat flour with ⅔ cup of all purpose.