Preheat oven to 400°F (200°C) and grease or line a standard 12-cup muffin tin with paper liners.

In a large mixing bowl, whisk together the all-purpose flour, cocoa powder, baking powder, baking soda, and salt. Stir in the granulated sugar.

In a separate medium bowl, whisk the eggs, milk, vegetable oil, and vanilla extract until the mixture is emulsified.

Create a well in the center of the dry ingredients and pour in the wet mixture. Use a rubber spatula to fold the ingredients together until just combined; do not overmix.

Gently fold 1 cup of the semi-sweet chocolate chips into the batter.

Distribute the batter evenly among the 12 muffin cups, filling each nearly to the top to encourage high domes.

Sprinkle the remaining 1/2 cup of chocolate chips over the tops of the batter in each cup.

Bake for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean or with only a few moist crumbs.

Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.