It's up to you really, I know people who use regular flour and don't have any problems with it. I use an organic wheat flour but honestly, the amount for the entire recipe is so small when you break it down to the actual amount they are going to consume at once in that tiny one inch square I don't think it makes that much of a difference. Wheat flour is probably better but I don't think regular flour used in a treat will hurt your dog at all...