Preheat oven to 350F with rack on lower middle position. Line baking sheet with parchment paper.
In a large bowl, whisk together flour, salt, baking soda, and cocoa.
In another large bowl or the bowl of stand mixer, combine butter, both sugars, and vanilla. Beat on medium-high until it's as fluffy as it can get, scraping sides down periodically; about 3-4 minutes. Add beaten eggs and beat just to combine.
Using rubber spatula, gently fold flour mixture into butter mixture just until batter is completely moistened. Fold in M&M's.
Wrap and chill dough until firm enough to handle, about 30 min to 1 hour.
Form dough into walnut sized balls and flatten slightly, as these tend not to spread too much. Place on parchment lined baking sheet and bake about 8 minutes. They'll seem a bit underdone, but will set up nicely when cool.