Prepare the oven: Preheat the oven to 375°F and line a 12-cup muffin pan with paper liners.
Combine the dry ingredients: Whisk the flour, baking powder, baking soda, and salt together in a medium bowl.
Make the peanut butter mixture: In a large bowl, whisk the peanut butter, brown sugar, granulated sugar, and oil until smooth.
Add the wet ingredients: Whisk in the eggs, Greek yogurt, milk, and vanilla until the mixture is creamy and evenly combined.
Make the batter: Add the dry ingredients to the wet mixture and gently fold until the flour is just incorporated. Avoid overmixing.
Add the chocolate chips: Fold in most of the chocolate chips, keeping a small amount aside for the muffin tops.
Fill the pan: Divide the batter evenly between the muffin cups, filling each about three-quarters full. Sprinkle the reserved chocolate chips over the tops.
Bake the muffins: Bake for 18–22 minutes, or until the tops are lightly golden and a toothpick inserted into the center comes out without wet batter.
Cool before serving: Let the muffins cool in the pan for about 5 minutes, then transfer them to a wire rack.