Preheat oven to 350°F. Line a 12-count muffin tin with paper liners. Set aside.
In a medium bowl, whisk the flour, cocoa powder, baking powder, salt, and baking soda together.
1¼ cups all-purpose flour, ¾ cup unsweetened cocoa powder, 1½ teaspoons baking powder, 1 teaspoon kosher salt, ½ teaspoon baking soda
In a large bowl, whisk the yogurt, sugar, oil, milk, and eggs together.
1 cup plain yogurt, ¾ cup granulated sugar, ½ cup vegetable oil, ⅓ cup milk, 2 large eggs
Add the dry ingredients to the wet ingredients and mix just until incorporated. Fold in the chocolate chips.
¾ cup semisweet chocolate chips
Fill the muffin liners no more than ⅔ full with chocolate batter.
Spoon an even amount of peanut butter (about ⅔ tablespoon) onto the chocolate batter in each individual muffin well. Use a toothpick to swirl the peanut butter and chocolate batter together.
½ cup peanut butter
Bake the muffins for 20-22 minutes, or until a toothpick inserted into the center comes out clean or with moist crumbs.
Let the muffins cool for 10 minutes in the tin, then transfer muffins to a cooling rack to cool completely. Serve and enjoy.