Preheat your oven to 350ºF and line a standard 12-cup muffin tin with paper cupcake liners.
In a medium bowl add flour, cocoa powder, baking powder and salt. Whisk to combine and set aside.
In a medium mixing bowl cream together butter and sugar, with an electric mixer or stand-mixer, until light and fluffy. Add eggs, one at a time, scraping batter down from sides of bowl in between each addition. Add vanilla and mix. With the mixer running on low slowly pour in half dry ingredients. Add yogurt and mix. Pour in the rest of the flour and mix until incorporated.
Fill each cupcake tin 2/3 full and bake until a toothpick inserted in the center comes out clean, about 20-25 minutes.
Cool in pan for 5 minutes then transfer to a wire rack to cool completely.
Once cooled cut a small hole in the middle of the cupcake and remove cake. Add about a tablespoon of cherry filling to each cupcake.