Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the cups lightly.
In a large mixing bowl, sift together the all-purpose flour, unsweetened cocoa powder, baking powder, baking soda, and salt.
Add the granulated sugar to the dry ingredients and mix until combined.
In a separate bowl, whisk together the eggs, whole milk, vegetable oil, and vanilla extract until smooth.
Pour the wet ingredients into the dry ingredients and stir gently until just combined. Do not overmix; the batter should be slightly lumpy.
Fold in the semi-sweet chocolate chips evenly throughout the batter.
Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full.
Sprinkle about 1/4 teaspoon of granulated sugar on top of each muffin for a slight crunchy topping.
Bake in the preheated oven for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean or with a few moist crumbs.
Remove the muffin tin from the oven and allow the muffins to cool in the tin for 5 minutes.
Transfer the muffins to a wire rack to cool completely before serving.