Preheat the oven to 375°F (190°C) and line a 12-cup muffin pan with liners.
In a large bowl, whisk together flour, sugar, baking powder, baking soda, and salt.
In another bowl, whisk milk, melted butter, eggs, and vanilla until smooth.
Pour wet ingredients into dry ingredients and gently mix until just combined.
Toss chocolate chips with flour and fold them into the batter.
Fill muffin cups ¾ full, sprinkle extra chocolate chips on top, and bake for 18–20 minutes.
Cool for 5 minutes before transferring muffins to a rack.