Preheat oven to 375℉. Spray a standard donut pan with coconut oil cooking spray or regular cooking spray. Combine flour, cocoa powder, baking soda, baking powder, and salt in a medium bowl. Whisk to combine. Set aside.
Gradually add the dry ingredients into the wet, folding to combine. Gently fold in the chocolate chips. Either using a pastry bag or a spoon, gently pipe or spoon the batter into the prepared donut pan. Fill each about 3/4 the way full. Bake for 12-15 minutes until donuts are cooked through and spring back when touched. Let cool on a baking rack.
While the donuts are baking, make the glaze. Add peanut butter and vanilla to a medium bowl. Whisk in the powdered sugar gradually, then add the almond milk and whisk until no lumps remain and a glaze forms. If it seems too thick, add an extra tablespoon of almond milk. Dip the donuts in the glaze, then sprinkle with chopped peanut butter cups. Devour.