Preheat oven to 350°F and line a 12-count muffin tin with paper liners.
In a medium bowl, whisk together flour, cocoa powder, baking powder, salt, and baking soda.
In a large bowl, whisk yogurt, sugar, oil, milk, and eggs until combined.
Add dry ingredients to wet ingredients and mix until just incorporated.
Fold in the chocolate chips gently.
Fill muffin liners about two-thirds full with chocolate batter.
Top each muffin with about two-thirds tablespoon of peanut butter and swirl it into the batter with a toothpick.
Bake for 20 to 22 minutes, or until a toothpick inserted in the center comes out clean or with moist crumbs.
Let muffins cool in the tin for 10 minutes, then transfer to a cooling rack to cool completely before serving.