In a large bowl, cream butter and sugars. Mix in egg and vanilla, followed by flours, cocoa powder, baking soda, baking powder and salt. Begin mixing on low, slowly increasing speed to medium. Mix until dough comes together and is smooth. Using a wooden spoon, mix in chocolate chips and M&Ms.
Cover and chill dough for 24 hours, allowing flavors to combine.
Remove dough 30+ minutes prior to baking.
Preheat oven to 350°F. Line baking sheets with silicone baking mats.
Form slightly larger than golfball sized balls of dough, spacing 2-inches apart. Bake for 13-15 minutes. Allow cookies to rest on baking sheet for 2 minutes prior to transferring to a cooling rack.
Store in an airtight container for up to several days.
Nutritional information is provided as a courtesy and is an estimate only. Nutrition information can vary for a variety of reasons. For the most accurate data, use your preferred nutrition calculator with the actual ingredients you used to make this recipe.
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