Preheat oven to 350 degrees and line baking sheets with silicone baking mats or parchment paper.
Mix flour, cocoa powder, baking soda, salt and coffee crystals in a bowl with a whisk. Set aside.
In the bowl of a stand mixer fitted with a paddle attachment, cream together the butter and sugar until pale and fluffy, 3 - 4 minutes.
Add eggs and vanilla and mix until well combined.
Add in the flour mixture and mix until dough comes together.
Stir in half the M&M's and chocolate chips by hand.
Scoop dough by rounded tablespoons onto prepared baking sheets. Place 3 reserved M&M's atop each cookie before baking.
Bake for 10 - 11 minutes, rotating pans halfway through baking time.
Allow to cool on baking sheets for 10 minutes before removing to wire cooling racks to finish cooling.