Yes! Because they're a lot bigger, I recommend breaking them up a bit first. Save some whole to use on top of the cookies, but place the rest in a zip-top bag and whack them with a rolling pin or give them a rough chop with a knife. The cookies will spread a bit more with the bigger M&Ms and won't hold a round shape as well as they do with mini M&Ms, but you can always scoot them into shape when they come out of the oven.