Preheat the oven to 350°F (175°C). Grease or line a muffin tin with paper liners.
Mix the dry ingredients: In a large mixing bowl, sift together the all-purpose flour, cocoa powder, baking powder, baking soda, and salt.
Whisk the wet ingredients: In another bowl, whisk together the eggs, milk, vegetable oil, and vanilla extract until smooth.
Combine wet and dry ingredients: Gradually pour the wet mixture into the dry ingredients, stirring gently until combined. Be careful not to overmix.
Add the chocolate chips: Fold in the chocolate chips and cocoa nibs (if using) until evenly distributed.
Scoop the batter: Spoon the batter evenly into the muffin tin, filling each cup about 2/3 full.
Bake the muffins: Place the tin in the preheated oven and bake for 18-20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.