These chocolate cheesecake cupcakes combine a soft cocoa cupcake with a cream cheese filling and a smooth ganache topping. Make the chocolate batter and cheesecake filling separately, layer them in a lined 12-cup muffin pan, and cool the cupcakes completely before adding the chocolate topping.
Cooking Time & Yield
- Prep Time: 20 minutes
- Bake Time: 20–22 minutes
- Cooling & Assembly: 30 minutes
- Total Time: ~1 hour 15 minutes
- Yield: 12 cupcakes
Ingredients
For the Chocolate Cupcakes
- 1 cup all-purpose flour
- ½ cup unsweetened cocoa powder
- 1 cup sugar
- 1 teaspoon baking soda
- ½ teaspoon baking powder
- ½ teaspoon salt
- 1 large egg
- ½ cup milk
- ½ cup vegetable oil
- ½ cup hot water
- 1 teaspoon vanilla extract
For the Cheesecake Filling
- 8 oz (225 g) cream cheese, softened
- ⅓ cup sugar
- 1 egg
- ½ teaspoon vanilla extract
For the Ganache Topping
- 1 cup semi-sweet chocolate chips
- ½ cup heavy cream
- Chocolate chunks or sprinkles (for garnish)
Instructions
Step 1: Prepare the Cupcakes
- Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
- In a large mixing bowl, whisk together the flour, cocoa powder, sugar, baking soda, baking powder, and salt.
- Add the egg, milk, vegetable oil, and vanilla extract. Mix until fully combined.
- Slowly stir in the hot water—this will thin out the batter, making it smooth and pourable.
Step 2: Make the Cheesecake Filling
- In a separate bowl, beat the softened cream cheese until smooth.
- Add sugar, egg, and vanilla extract. Mix until creamy and lump-free.
Step 3: Assemble the Cupcakes
- Add a shallow layer of chocolate batter to each liner, leaving plenty of room for the filling and the remaining batter.
- Divide the cheesecake filling evenly among the 12 liners, spooning it into the center of each.
- Add a little more chocolate batter on top, just enough to cover the cheesecake (avoid overfilling).
Step 4: Bake
- Place the muffin tin in the oven and bake for 20–22 minutes, until the cheesecake centers are set and a toothpick inserted in the chocolate cake portion comes out clean.
- Let the cupcakes cool completely on a wire rack before topping.
Step 5: Make the Ganache
- Heat the heavy cream in a small saucepan until it just begins to simmer.
- Pour over the chocolate chips and let sit for 1–2 minutes.
- Stir until smooth and glossy, then allow to cool slightly so it thickens.
Step 6: Top & Garnish
- Spread the ganache over the cooled cupcakes.
- Garnish with the listed chocolate chunks or sprinkles, if desired.
Tips for Perfect Results
- Do not overfill: Leave room in the liners for the cheesecake filling to bake evenly.
- Room temperature cream cheese: Ensures a smooth cheesecake layer without lumps.
- Cooling time: Allow cupcakes to cool fully before adding ganache, otherwise it will melt.
- Flavor twist: Add a spoonful of raspberry jam or peanut butter with the cheesecake layer for a surprise inside.
Estimated Nutrition (per cupcake)
- Calories: ~280 kcal
- Carbohydrates: 32 g
- Protein: 5 g
- Fat: 15 g
- Sugar: 22 g
(Values may vary depending on toppings and exact ingredients used.)
Storage and Make-Ahead Tips
Because the filling contains cream cheese and the topping contains cream, keep the cooled cupcakes covered in the refrigerator. Add the ganache only after the cupcakes have cooled completely. For serving, let the topping soften slightly while keeping the cheesecake center cool.
Frequently Asked Questions
How do I keep the cheesecake filling smooth?
Use softened cream cheese. Beat it smooth before adding sugar, egg and vanilla, then divide the filling evenly among the liners.
Why do my cupcakes overflow?
The batter and cheesecake filling both take up space. Start with a shallow layer of batter, add the filling and leave room at the top when adding the final chocolate layer.
How do I check doneness?
Check that the cheesecake center is set, then test the chocolate cake portion with a toothpick. Do not judge by a toothpick pushed through the creamy filling alone.
Can I make the cupcakes before adding ganache?
Yes. Bake and cool them, then refrigerate covered. Add the cooled, thickened ganache before serving.