Preheat the oven to 400 (F) and prepare two muffin tins by lining each cavity with its own muffin liner.
In a medium bowl, whisk together 2 cups plus 2 tablespoons all-purpose flour, 3/4 cup unsweetened natural cocoa powder, 1 tablespoon baking powder, 1/2 teaspoon baking soda, and 1/4 teaspoon salt until combined. Set aside.
In a large bowl, whisk together 2 large eggs and 1 1/4 cups granulated sugar until a pale yellow. Add 1 cup buttermilk, 1/2 cup melted unsalted butter and 1 teaspoon pure vanilla extract and whisk until just combined.
Sprinkle the dry ingredients (from the 2nd step) evenly onto the surface of the wet ingredients (from the 3rd step). Use a rubber spatula to fold until combined, with one or two flour streaks left in the batter. Add 3 ounces dark chocolate chunks and 1 ounce mini chocolate chips (reserve the rest of the chocolate) and fold into the batter until just combined. DO NOT OVERMIX.
Divide the batter between 24 liners, using a 1 tablespoon cookie dough scoop to spoon about 2 tablespoons of batter per liner or at least until the liners are 2/3s of the way full. Sprinkle the tops of each muffin with the remaining chocolate pieces.
Bake in the preheated oven for 18 to 21 minutes or until the tops look set and a skewer inserted into the center of a muffin comes out almost clean. Allow the muffins to cool in the tin on a wire rack for 10 minutes, before turning out onto the wire rack to cool completely.
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