Cakes and Cupcakes/ Recipes

Black Bottom Cupcakes with Ganache

Dark chocolate cake with a cream cheese filling get dressed up when topped with ganache. These Black Bottom Cupcakes with Ganache are the perfect-sized indulgent treat!

black bottom cupcakes with ganache

Aren’t cupcakes awesome? Little, portion-controlled, single serve desserts all wrapped up in their own little paper! There are SO many varieties of cupcakes out there. This recipe for Black Bottom Cupcakes, with its creamy cheesecake filling was one of my favorite things to bake and eat when I was growing up. Today, I have dressed them up a bit with a rich ganache frosting to make them extra special. No time to make ganache? You can certainly serve these without it…they are THAT good!

black bottom cupcakes

Homemade chocolate cake is just so rich and chocolatey and this particular recipe is SO easy, that there’s no excuse to cheat and use a box mix.  You can use regular cocoa powder or dark, depending on how dark you want your cake to be. I typically use regular cocoa, as the coffee in the recipe brings out the full chocolate flavor. You mix the batter all in one bowl and if you have a whisk, you can even mix it up by hand.

The creamy center is made with cream cheese, sugar and egg, just like cheesecake. The key is you need to be sure your cream cheese is softened. You don’t want lumps in your filling. If you forgot to soften your cream cheese ahead of time, simply unwrap it and place it on a microwave-safe plate. Heat it on HIGH for 10 seconds. Remove and press the center to see if it has softened. If not, return to microwave and repeat with 10 second intervals until softened. No microwave? No worries! Unwrap the cream cheese, cut it into 1 inch cubes and let stand for 30 minutes to an hour.  How easy is that?

black bottom cupcakes

Once your chocolate batter and filling are made, you just spoon it all into the pan. Fill the cupcake tins about half full. Then simply spoon the filling in the center of each. The liners are going to be almost full at this point. But don’t worry, the cheesecake filling settles down into the cupcake and the chocolate batter rises up around it. The toothpick test doesn’t work asweel for these little gems, so check their doneness by lightly touching them with your finger and seeing if it springs back. The cheesecake filling should also look set on top.

At this point, you can be done and serve the  Black Bottom cupcakes like this. They are REALLY good on their own. But if you want to make them a little fancier, (we like things fancy) then make the ganache. Just two ingredients needed here: whipping cream and good quality semisweet chocolate. It takes the ganache a little while to cool to a spreading consistency, so it’s good to make it while the cupcakes are cooling.

That’s it! Easy-Peasy-Oh-So-Fudgy-Cheesecake-Filled Black Bottom Cupcakes with Ganache.  They were a favorite in our house and sure to be a favorite in yours! Happy Baking!

Tips and Tricks for Your Best Baking:

  • Be sure your cream cheese is completely softened.
  • Don’t pack your flour into the cup when measuring or your cupcakes will be dry and heavy.
  • Don’t overmix your cupcake batter; mix just until blended.
  • Use pure chocolate for ganache.
  • Let cupcakes cool completely before topping with ganache, or ganache will melt.

Yields 20 cupcakes

Black Bottom Cupcakes with Ganache

20 minPrep Time

30 minCook Time

2 hrTotal Time

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  • Filling:
  • 1 (8-oz.) pkg. cream cheese, softened
  • 1/3 cup sugar
  • 1 egg
  • 1 cup mini chocolate chips
  • Cupcakes:
  • 1 1/2 cups flour
  • 1 cup sugar
  • 1/4 cup cocoa
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 cup coffee, cooled
  • 1/2 cup vegetable oil
  • 1 tablespoon vinegar
  • 1 teaspoon vanilla
  • Ganache:
  • 3/4 cup whipping cream
  • 8 ounces semisweet chocolate, coarsely chopped


  1. Heat oven to 350 degrees F. Line muffin pan with 20 paper muffin cups or spray lightly with cooking spray; set aside.
  2. In medium bowl, combine cream cheese, 1/3 cup sugar and egg; mix well. Stir in mini chocolate chips; set aside.
  3. In large bowl, stir together flour, 1 cup sugar, cocoa, baking soda and salt.
  4. Make a well in the center and add coffee, oil, vinegar and vanilla; mix until blended.
  5. Spoon chocolate batter into prepared muffin pan, filling cups about half full.
  6. Spoon filling mixture into center of each cupcake.
  7. Bake at 350 degrees F. for 25-30 minutes, until cupcake springs back when lightly touched and centers are set.
  8. Let stand 5 minutes in pan; remove cupcakes from pan and cool completely.
  9. While cupcakes are cooling, make ganache: In small saucepan, heat cream over medium heat, stirring often, until cream is just about to boil. Remove from heat and add chopped chocolate; let stand 3 minutes. Stir until smooth and melted.
  10. Let cool, stirring often, until thickened to a spreading consistency. If desired, to speed cooling, place ganache in refrigerator for 30 minutes. Stir and return to refrigerator. Stir ever 15 minutes until desired consistency is reached. Spread over cooled cupcakes.

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