If you adore the rich, luscious combination of cheesecake and chocolate, then this Cheesecake Stuffed Chocolate Cupcakes Recipe is about to become your new favorite treat. Each bite delivers moist, chocolatey cupcake goodness with a surprise creamy cheesecake center that tastes indulgent yet delightfully balanced. These cupcakes bring together the best of two worlds, perfect for impressing guests or simply enjoying a moment of decadent bliss. Trust me, once you try this recipe, reaching for store-bought desserts will be a thing of the past.

Ingredients You’ll Need
The magic of this Cheesecake Stuffed Chocolate Cupcakes Recipe lies in its simple yet thoughtfully chosen ingredients. Each one plays a crucial role in achieving the perfect texture, taste, and appearance of the cupcakes.
- Semisweet chocolate chips (2 cups, divided): Adds rich chocolate flavor with melty pockets of gooey goodness throughout.
- All-purpose flour (1 1/2 cups): The foundation providing structure and softness to the cupcakes.
- Baking soda (1 teaspoon): Gives the cupcakes a light and airy lift.
- Salt (1/2 teaspoon plus 1/8 teaspoon): Enhances all the flavors and balances the sweetness.
- Granulated sugar (3/4 cup total): Sweetens both the cake and creamy cheesecake filling.
- Vegetable oil (1/3 cup): Keeps the cupcakes unbelievably moist.
- Eggs (2 large): Bind the ingredients and add richness.
- Vanilla extract (1 teaspoon): Elevates the flavor with warm, sweet notes.
- Water (1 cup): Activates the baking soda and hydrates the batter for softness.
- Cream cheese (6 ounces, room temperature): The star ingredient for that velvety cheesecake center.
How to Make Cheesecake Stuffed Chocolate Cupcakes Recipe
Step 1: Preheat and Prepare
Start by heating your oven to 350 degrees Fahrenheit (175 degrees Celsius). Line two muffin tins with paper liners—this not only keeps the cupcakes clean and easy to handle but gives them that classic presentation you love.
Step 2: Melt Half the Chocolate
Take half a cup of the semisweet chocolate chips and melt them gently in the microwave. Give them a minute or so, stirring intermittently, until smooth. Set aside and allow the chocolate to cool slightly, so it blends perfectly without scrambling the eggs in the batter later.
Step 3: Combine Dry and Wet Ingredients
Whisk together the flour, baking soda, and salt in a bowl—these dry ingredients will give the cupcake its structure and lift. In another bowl, combine granulated sugar, vegetable oil, the large egg, and vanilla extract. Add the melted chocolate and water alternately to the dry ingredients, mixing just until blended. The batter will be thinner than usual, but that’s exactly how you want it for ultra-moist cupcakes.
Step 4: Make the Cheesecake Filling
Using a stand mixer or hand mixer, beat the cream cheese, sugar, egg, and salt until creamy and smooth. Then stir in one full cup of the semisweet chocolate chips. This luscious filling is where the magic happens—melty, creamy, and studded with chocolate chunks.
Step 5: Assemble the Cupcakes
Fill each muffin cup halfway with the chocolate cupcake batter. Next, dollop about one tablespoon of cheesecake filling right in the center of each one. Carefully, cover the cheesecake with the remaining chocolate batter. This layering creates that delightful surprise when you bite into the cupcakes!
Step 6: Bake and Finish with Chocolate
Bake the cupcakes for 20 to 25 minutes until a toothpick inserted in the cake portion comes out clean (watch not to pierce the cheesecake center). While the cupcakes are still hot, sprinkle the remaining chocolate chips over the top. They’ll melt and form a naturally glossy, homemade chocolate frosting that’s simply irresistible.
Step 7: Cool Completely
Allow the cupcakes to cool in the pan initially before transferring them to a wire rack to cool fully. This final step ensures the cupcakes set perfectly and the flavors meld beautifully, ready for you to enjoy.
How to Serve Cheesecake Stuffed Chocolate Cupcakes Recipe

Garnishes
Want to take these cupcakes to the next level? Sprinkle a little powdered sugar on top or add fresh raspberries for a burst of tartness that complements the rich chocolate and creamy cheesecake perfectly. A drizzle of caramel or a dollop of whipped cream is also an elegant touch.
Side Dishes
Serve alongside a scoop of vanilla bean ice cream or a rich coffee for a dessert experience that feels café-worthy. A simple fresh fruit salad can provide a refreshing contrast to the cupcake’s decadence.
Creative Ways to Present
Try serving the cupcakes in mini paper cups for a bite-sized party version, or stack them on a tiered dessert tray for special occasions. Wrapping each one with a decorative ribbon adds charm if you’re gifting them to friends or family.
Make Ahead and Storage
Storing Leftovers
Place any uneaten cupcakes in an airtight container and store them in the refrigerator. They’ll keep beautifully for up to 3 days, maintaining their moist texture and creamy filling.
Freezing
You can freeze these cupcakes for longer storage. Wrap each cupcake tightly in plastic wrap and place them in a freezer-safe bag or container. They’re best enjoyed within 2 months for optimal freshness.
Reheating
When ready to enjoy, thaw frozen cupcakes in the refrigerator overnight. Warm them slightly in the microwave for about 15 seconds to bring back that freshly baked feel and gooey chocolate delight.
FAQs
Can I use different types of chocolate chips?
Absolutely! While semisweet chocolate chips provide a perfect balance, you can experiment with dark, milk, or even white chocolate chips to tailor the cupcakes to your preference.
Is it necessary to use vegetable oil?
Vegetable oil helps keep the cupcakes moist and tender. However, you can substitute with another neutral oil like canola or even melted coconut oil if preferred, but avoid solid fats like butter as they change the texture.
Can I make the cheesecake filling ahead of time?
Yes! You can prepare the cheesecake filling a day in advance and keep it refrigerated. Just give it a quick stir before assembling the cupcakes to keep it smooth.
Why is the batter thin? Is this normal?
Yes, the batter will be thinner than a typical cupcake batter due to the water and oil content, but this results in an incredibly moist and tender cupcake, so don’t worry—this is exactly how it should be.
How do I know when the cupcakes are done without piercing the cheesecake?
Insert a toothpick near the edge of the cupcake, avoiding the center cheesecake portion. It should come out clean from the cake area, indicating the cupcakes are perfectly baked.
Final Thoughts
If you want to delight your loved ones with a dessert that marries two all-time favorites—chocolate and cheesecake—this Cheesecake Stuffed Chocolate Cupcakes Recipe is an absolute must-try. It’s easy enough for any home baker yet impressive enough to steal the show at any gathering. Put on your apron and enjoy every rich, creamy, and chocolatey bite of these incredible cupcakes!
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Cheesecake Stuffed Chocolate Cupcakes Recipe
- Total Time: 40 minutes
- Yield: 16 cupcakes 1x
Description
Indulge in these decadent Cheesecake Stuffed Chocolate Cupcakes, combining rich chocolate cupcake batter with a creamy cheesecake center. Topped with melted chocolate chips as a glossy frosting, these cupcakes offer a delightful contrast of flavors and textures, perfect for any celebration or dessert craving.
Ingredients
Chocolate Cupcake Batter
- 2 cups (340 grams) semisweet chocolate chips, divided
- 1 1/2 cups (187 grams) all-purpose flour
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 1/2 cup (100 grams) granulated sugar
- 1/3 cup (66 grams) vegetable oil
- 1 large egg
- 1 teaspoon vanilla extract
- 1 cup water
Cheesecake Filling
- 6 ounces (170 grams) cream cheese, at room temperature
- 1/4 cup (50 grams) granulated sugar
- 1 large egg
- 1/8 teaspoon salt
- 1 cup semisweet chocolate chips
Instructions
- Preheat and Prepare Muffin Tins: Preheat your oven to 350°F (175°C). Line two muffin tins with 16 paper cupcake liners to prepare for baking.
- Melt Chocolate: Melt 1/2 cup of semisweet chocolate chips in the microwave using short bursts, stirring in between to avoid burning. Allow the melted chocolate to cool slightly.
- Make Chocolate Batter: In a medium bowl, whisk together the flour, baking soda, and salt. In another large bowl, combine the sugar, vegetable oil, egg, and vanilla extract. Gradually add the melted chocolate and water alternately with the flour mixture into the wet ingredients, mixing until smooth. Note the batter will be thin.
- Prepare Cheesecake Filling: Using a mixer, beat together the cream cheese, sugar, egg, and salt until the mixture is smooth and creamy. Gently fold in 1 cup of semisweet chocolate chips to the cheesecake mixture.
- Assemble Cupcakes: Spoon chocolate cupcake batter halfway into each lined muffin cup. Add about 1 tablespoon of the cheesecake filling on top of the batter in each cup. Then, cover with the remaining chocolate batter, filling the cups almost to the top.
- Bake: Place the muffins in the preheated oven and bake for 20–25 minutes, until a toothpick inserted near the edge comes out clean.
- Top with Melting Chocolate: Immediately after removing the cupcakes from the oven, sprinkle the remaining chocolate chips over the hot cupcakes. Allow the residual heat to melt the chips, then spread evenly over the tops to create a glossy chocolate frosting.
- Cool and Serve: Let the cupcakes cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely. Serve at room temperature.
Notes
- For best results, ensure the cream cheese is at room temperature to avoid lumps in the filling.
- If you prefer, you can substitute vegetable oil with melted butter for a richer flavor.
- Do not overbake the cupcakes; they are done when a toothpick inserted near the edge is just clean.
- Store leftover cupcakes in an airtight container in the refrigerator and bring to room temperature before serving.
- The melted chocolate frosting will harden as it cools; for a shinier finish, you may reheat gently before serving.
- Prep Time: 15 minutes
- Cook Time: 25 minutes
- Category: Dessert
- Method: Baking
- Cuisine: American