Preheat oven to 325 degrees. Grease muffin pan or line with paper liners.
In a large bowl, combine the flour, sugar, cocoa, baking soda, and salt. Mix to combine.
Make a well in the middle of the dry ingredients and pour in the eggs, yogurt, milk, oil, and vanilla extract. Stir until combined. There will still be a few lumps.
Fold in 1 cup mini chocolate chips.
Scoop in to muffin cups to fill to ⅔ full. Sprinkle with remaining 2 tablespoon mini chocolate chips.
Bake 20 minutes. Cool in muffin tin 10 minutes before removing to wire rack to finish cooling.
Enjoy!