Position rack in the center of the oven, then preheat to 375°F. Line a 12-cup muffin pan with 10 paper liners or spray with oil.
Whisk flour, cocoa powder, sugar, baking powder, and salt in a large bowl.
In a medium bowl, whisk yogurt, oil, milk, eggs, and vanilla until smooth. Stir the yogurt mixture into the flour mixture until 80% incorporated.
Fold in chocolate chips. Divide batter evenly between muffin cups.
Bake 20 to 25 minutes, until the tops spring back when gently pressed or an instant-read thermometer reaches 190°F. Cool in pan a few minutes, then transfer to a rack.
Notes
Flour: Spoon and level your flour to avoid dry muffins, or use the "Metric" button in the recipe card to measure by weight (which is most accurate!).Milk: Whole milk gives a tender, rich crumb. Any milk works, including Barista Oat Milk for a dairy-free option.Storage: Muffins can be stored in an airtight container at room temperature for 3 days or frozen for up to 3 months. Reheat in a microwave for 15–20 seconds to soften.Batch Size: For taller, bakery-style muffins, make 10 muffins. To make 12, reduce bake time to 18–20 minutes.