Preheat oven to 325⁰F. Line a muffin tin with paper liners. Whisk together flour, baking powder. Put butter and chocolate in the top half of a double boiler over hot, simmering water; stir until melted. Remove from heat and let cool slightly.
Whisk granulated sugar into cooled chocolate mixture. Add eggs and whisk until mixture is smooth. Stir in vanilla. Add flour mixture; stir until well incorporated.
Make the peanut butter filling: stir together all filling ingredients until smooth.
Spoon 2 tablespoons chocolate batter into each lined cup, followed by 1 tablespoon peanut butter filling. Repeat with additional tablespoon batter and top with 1 teaspoon filling. Swirl top of cupcake batter and filling with a wooden skewer or toothpick.
Bake, rotating halfway through, until a cake tester inserted in the centers comes out with only a few moist crumbs attached, about 40 minutes. Transfer to a wire rack to cool completely before removing cupcakes.