Preheat the oven to 350 degrees and line a baking sheet with parchment paper.
Mix dry ingredients less the sugars in a large mixing bowl (flours, cocoa powder, baking soda, salt).
Using a standing mixer on low speed, cream the sugars and butter. After stopping the mixer and scraping down the sides, increase to medium speed for about 3 minutes until fluffy.
Add vanilla, egg, and mix again until combined.
Slowly add in the dry ingredients until combined.
Form dough into round balls about 1.5 inches in side and place on parchment paper.
Press your orange mini M&Ms gently into the cookie balls.
Bake for 10 minutes. The recipe makes about 18-19 cookies so you will likely have to bake in two batches.