Preheat oven to 325-degrees and line 2 baking sheets with parchment paper.
Whisk together flour, cocoa powder, baking soda, and salt in a medium bowl; set aside.
In another heat-proof bowl, melt the chocolate chips and butter in the microwave, stirring every 30 seconds until smooth. Into the chocolate mixture, beat the sugar, eggs and vanilla until combined.
Carefully add in the flour mixture and fold in the M&M candies.
Use a 1-½ inch cookie scoop and placed the dough balls about 2 inches apart. Bake for about 15 minutes until the cookies are begin to crack, then remove to a cooling rack.
Cookies can be stored in an airtight container for 2-3 days - but trust me that these are the most delicious right out of the oven when the M&M's are still melty in the middle - so good!