Preheat oven to 400 degrees and spray a muffin tin with cooking spray.
In a medium bowl, mix together the flour, cocoa powder, baking powder, baking soda and salt. Set aside
In a large, microwave safe bowl, melt the peanut butter until smooth - about 1 minute. Whisk in the yogurt, stevia, coconut sugar, egg , extract and milk until well combined.
Slowly fold the dry ingredients into the wet ingredients, followed by the peanut butter chips, stirring until just moistened. Cover and refrigerate 30 minutes
Using an extra large cookie scoop (or just a plain old spoon) divide the batter evenly among the greased muffins tins, filling almost all the way to the top.
Sprinkle with extra peanut butter chips if desired and bake for 5 minutes. Then, reduce the oven temp to 375 degrees and bake another 14-16 minutes, or until a tooth pick comes out clean.
Let the muffins cool in the pan for 5 minutes (if you can resist) and then transfer to a cooling rack to finish cooling.