Line a baking sheet with parchment paper or a silicone baking mat.
In the bowl of an electric mixer, beat butter until light and creamy. Add in sugar and brown sugar and beat until well combined. Add in eggs, one at a time, mixing until each is fully incorporated into batter. Add in vanilla and mix.
In a separate bowl, combine flours, cocoa powder, baking soda and salt. Slowly add dry mixture to wet mixture, mixing until just combined. Stir in M&Ms and chocolate chips.
Using a large cookie scoop, scoop cookie dough onto baking sheet. A large cookie scoop holds about 3 tablespoons of cookie dough. Space dough at least 2″ apart.
Bake for approximately 10-12 minutes. Cookies should be starting to firm up but still soft in the middle. Remove from oven and allow to cool on pan on a wire rack for at least five minutes. Repeat with remaining dough. Allow to cool completely prior to storing. Store in an airtight container.