
The Ultimate Chocolate Cheesecake Cupcakes: A Decadent Duo
By Jason Griffith
If you have ever found yourself torn between a rich, moist chocolate cake and a creamy, tangy cheesecake, I have the perfect solution for you. These Chocolate Cheesecake Cupcakes are the absolute best of both worlds. Imagine a deep cocoa-flavored cupcake that hides a luscious cream cheese surprise inside, all topped off with a silky, professional-grade chocolate ganache.
Whether you are hosting a birthday party, a holiday gathering, or just need a little mid-week pick-me-up, these cupcakes deliver a “wow” factor without requiring professional pastry chef skills. They are sophisticated enough for a formal event but simple enough to bake with the kids on a rainy afternoon.
Why I Love This Recipe
There is something magical about the texture contrast here. The chocolate batter uses hot water, which “blooms” the cocoa powder for a deeper flavor and creates an incredibly tender crumb. When that hits the dense, velvety cheesecake center, it’s pure bliss.
Unlike some complicated stuffed desserts, this recipe is incredibly forgiving. If you love decadent treats as much as I do, you might also find yourself obsessed with these chocolate chip cookie dough brownie bombs or perhaps my secret weapon for parties: these cake mix cookies. But today, it’s all about the chocolate and cheese!
Ingredients You’ll Need
For the Cupcakes:
- 1 cup all-purpose flour: The sturdy base for our chocolate cake.
- ½ cup cocoa powder: Use high-quality unsweetened cocoa for the best results.
- 1 cup sugar: To balance the bitterness of the cocoa.
- 1 tsp baking soda & ½ tsp baking powder: Our leavening agents for that perfect rise.
- ½ tsp salt: To enhance all the chocolate flavors.
- 1 large egg: Room temperature works best for emulsifying.
- ½ cup milk: Provides moisture and fat.
- ½ cup vegetable oil: Keeps the cupcakes moist for days.
- ½ cup hot water: The secret to a smooth, deep chocolate batter.
- 1 tsp vanilla extract: For that classic bakery aroma.
For the Cheesecake Filling:
- 8 oz (225 g) cream cheese: Must be softened to avoid lumps!
- ⅓ cup sugar: Just enough sweetness to compliment the tang.
- 1 egg: To set the cheesecake center as it bakes.
- ½ tsp vanilla extract: For depth of flavor.
For the Ganache Topping:
- 1 cup semi-sweet chocolate chips: The crown of the cupcake.
- ½ cup heavy cream: To create that glossy, pourable texture.
- Chocolate chunks or sprinkles: For the final decorative touch.
Swaps and Notes
- The Oil: You can substitute the vegetable oil with melted coconut oil or even applesauce if you’re looking for a slightly lighter version.
- The Milk: Any dairy or non-dairy milk (like almond or oat) will work perfectly here.
- Cream Cheese: Always use the full-fat block style cream cheese. The “whipped” version or low-fat spreads won’t set properly in the oven.
- Sugar: If you want a deeper flavor, you can swap the white sugar in the cupcake batter for light brown sugar.
Step-by-Step Instructions
1. Prep the Station
Preheat your oven to 350°F (175°C). Line a standard 12-cup muffin tin with your favorite paper liners.
2. Mix the Dry and Wet
In a large mixing bowl, whisk together the flour, cocoa, sugar, baking soda, baking powder, and salt. Add the egg, milk, oil, and vanilla extract. Mix until just combined.
3. The “Bloom”
Slowly pour in the hot water. Don’t be alarmed—the batter will be very thin! This is exactly what we want for a moist, tender cupcake. Stir gently until smooth.
4. Prepare the Cheesecake Heart
In a separate medium bowl, beat the softened cream cheese, sugar, egg, and vanilla. Use an electric hand mixer to ensure it is completely smooth and creamy. If you love this flavor profile, you’ll also enjoy the best peanut butter brownies which also feature a creamy layer!
5. Assemble the Cupcakes
Fill your cupcake liners about halfway with the chocolate batter. Spoon approximately 1 tablespoon of the cheesecake mixture directly into the center of each. Carefully top with a little more chocolate batter. Be careful not to fill the liners more than ¾ of the way to the top.
6. Bake and Cool
Bake for 20–22 minutes. You’ll know they are done when the tops spring back slightly when touched. Let them cool in the pan for 5 minutes before moving them to a wire rack to cool completely.
7. The Glossy Ganache
Heat your heavy cream in the microwave or on the stove until it just begins to simmer. Pour it over your chocolate chips and let it sit for 2 minutes. Stir until it’s a smooth, shiny liquid. Let it cool for a few minutes to thicken slightly, then spread or dip the tops of the cupcakes. Garnish immediately with chocolate chunks or sprinkles!
Tips for Success
- Don’t Overbake: These cupcakes continue to set as they cool. Overbaking can lead to a dry cake and a rubbery cheesecake center.
- Room Temperature Ingredients: Make sure your cream cheese and eggs are at room temperature. This ensures the cheesecake filling is silky smooth and the batter doesn’t “break.”
- Hot Water Tip: Use very hot tap water or water heated just before boiling to properly dissolve the cocoa.
Serving Suggestions and Pairings
These cupcakes are a dessert powerhouse on their own, but they pair beautifully with a cold glass of milk or a stiff espresso. If you’re serving these at a party, consider a “dessert bar” approach. Pair them with these chocolate chip cookie bites for a variety of textures!
Storage and Leftover Tips
Because of the cream cheese filling, these cupcakes should be stored in an airtight container in the refrigerator. They will stay fresh and delicious for up to 4 days. If you prefer them at room temperature, just take them out of the fridge about 20 minutes before serving.
Can you freeze them? Yes! These freeze beautifully. Wrap them individually in plastic wrap and place them in a freezer bag for up to 2 months. Thaw in the fridge overnight.
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Final Thoughts
These Chocolate Cheesecake Cupcakes are truly a labor of love that doesn’t actually require much labor! They are the ultimate crowd-pleaser and a staple in my baking rotation.
Did you try this recipe? I would love to hear how they turned out! Leave a comment below, and don’t forget to follow Chefmaniac on social media for more decadent recipes and kitchen tips.




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