Preheat oven to 350 degrees.
Using a stand mixer fitted with the paddle attachment or a hand mixer, cream the butter and sugar on high for 2-3 minutes. Scrape down the bowl once complete.
Add in eggs, vanilla extract and peanut butter. Mix until combined. Scrape down the bowl once complete.
In separate bowl, whisk dry ingredients together (oats, baking soda, salt).
Add dry ingredients to wet ingredients. Mix until combined.
Using a wooden spoon, mix in the chocolate chips and m&m's.
Chill dough in refrigerator for 30 minutes.
Grease muffin tin well (12 count or 2 6-count tins).
Use a spoon or cookie dough scoop to fill each muffin well. Gently press the dough down with your fingers. Each muffin well should be about ½-¾ full of dough.
Bake for 12-15 minutes or until edges of the cookie cups are slightly browned.
Once you remove the cookies from the oven, immediately use a teaspoon or tablespoon measuring spoon to make an indent in the center of the cookie cups.
Set aside and let them cool for at least an hour (until they reach room temperature). Make ganache while cookies cool.