If you have a serious sweet tooth and love the perfect marriage of rich chocolate with creamy cheesecake, you are absolutely going to fall in love with this Cheesecake Stuffed Chocolate Cupcakes Recipe. Imagine biting into a moist, deeply chocolatey cupcake that hides a luscious, velvety cheesecake core inside—every mouthful is a delightful surprise. Whether you’re baking for a family gathering, a special celebration, or just because you deserve a treat, these cupcakes bring comfort and indulgence together in the most irresistible way.

Ingredients You’ll Need
Every ingredient in this recipe plays an essential role, from building the tender chocolate cupcake base to crafting the smooth cheesecake center. They come together effortlessly to create a balance of flavors and textures that will wow anyone who tries these. Let’s take a look at what you’ll need to whip up these beauties:
- Semisweet chocolate chips (2 cups): Provides the rich chocolate flavor and a melty, fudgy texture in both batter and topping.
- All-purpose flour (1 1/2 cups): The foundation that gives cupcakes their structure and fluffiness.
- Baking soda (1 teaspoon): Helps your cupcakes rise perfectly and become light.
- Salt (1/2 teaspoon): Enhances all the chocolatey goodness and balances sweetness.
- Granulated sugar (1/2 cup plus 1/4 cup for cheesecake): Sweetens both the cupcake and the cheesecake filling.
- Vegetable oil (1/3 cup): Keeps the cupcakes moist and tender.
- Large eggs (2 total): Provides structure and richness, one for cupcakes and one for cheesecake.
- Vanilla extract (1 teaspoon): Adds warmth and depth to the chocolate flavor.
- Water (1 cup): Keeps batter thin and ensures moist cupcakes.
- Cream cheese (6 ounces, room temperature): Creates that creamy, dreamy cheesecake center everyone loves.
How to Make Cheesecake Stuffed Chocolate Cupcakes Recipe
Step 1: Prepare Your Oven and Baking Pans
Start by heating your oven to 350°F (175°C) and lining two muffin tins with paper liners. This helps keep the cleanup minimal and the cupcakes from sticking, so you get perfect individual portions every time.
Step 2: Melt Your First Batch of Chocolate Chips
Gently melt 1/2 cup of your semisweet chocolate chips in the microwave in short bursts, stirring often to avoid burning. Let it cool slightly before adding to the batter to ensure it blends smoothly without cooking the eggs.
Step 3: Mix the Dry and Wet Ingredients for the Cupcake Batter
In one bowl, whisk together the flour, baking soda, and salt to evenly distribute the leavening and seasoning. In another, combine the granulated sugar, vegetable oil, egg, and vanilla, then alternate adding the melted chocolate and water with the flour mixture. Expect this batter to be on the thinner side—that’s exactly what makes the cupcakes so moist and tender.
Step 4: Whip Up the Cheesecake Filling
Using a mixer, beat the cream cheese with the 1/4 cup sugar, an egg, and a pinch of salt until silky smooth. Then fold in a whole cup of chocolate chips. This fudge-filled cheesecake will be your jackpot surprise inside the cupcakes.
Step 5: Assemble the Cupcakes
Fill each muffin cup halfway with the chocolate batter, add about a tablespoon of cheesecake filling in the center, then cover with the remaining batter. This layering ensures a perfect cheesecake center sealed inside every cupcake.
Step 6: Bake and Add the Final Chocolate Touch
Bake for 20 to 25 minutes until the cupcakes are set. While they are still hot, sprinkle the leftover chocolate chips on top—they’ll melt slightly, creating an elegant, glossy chocolate finish that acts like a natural frosting.
Step 7: Cool Before Enjoying
Allow the cupcakes to cool in the pan for a bit before transferring them to a wire rack to cool completely. This step is key to letting the cheesecake inside firm up just enough for the perfect bite.
How to Serve Cheesecake Stuffed Chocolate Cupcakes Recipe

Garnishes
Keep it simple and classy by dusting your cupcakes with a light sprinkle of powdered sugar or cocoa powder. For a fancy twist, add fresh berries or a dollop of whipped cream. These touches brighten the rich chocolate and tangy cheesecake flavors, making each cupcake look as good as it tastes.
Side Dishes
Serving these cupcakes alongside a fresh fruit salad or a scoop of vanilla ice cream can balance the indulgence with refreshing notes. You could also pair them with a hot cup of coffee or a glass of cold milk to complement the chocolate’s intensity perfectly.
Creative Ways to Present
For a party, arrange your cupcakes on a tiered stand with edible flowers and chocolate shavings for an eye-catching dessert table. Wrapping each cupcake in a colorful paper or presenting them in clear cellophane bags tied with a ribbon makes them wonderful gift ideas for friends or coworkers.
Make Ahead and Storage
Storing Leftovers
Store your cheesecake stuffed chocolate cupcakes in an airtight container at room temperature for up to two days. If you prefer, refrigerate them to keep the cheesecake filling fresh longer, just allow them to return to room temperature before serving for optimal taste.
Freezing
You can freeze these cupcakes to enjoy later by wrapping each one individually in plastic wrap and placing them in a freezer-safe container. Frozen cupcakes last up to a month. Thaw them overnight in the fridge before serving.
Reheating
For that freshly baked warmth, gently reheat cupcakes in the microwave for 15-20 seconds or place them in a warm oven for a few minutes. This brings back the melty texture of the chocolate and the creamy cheesecake in the center.
FAQs
Can I make these cupcakes dairy-free?
While this recipe relies on cream cheese for the cheesecake filling, you can experiment with dairy-free cream cheese alternatives. Just be aware that the texture and flavor may change slightly, but they should still be delicious!
Can I use dark chocolate instead of semisweet chocolate chips?
Absolutely! Using dark chocolate chips will give your cupcakes a richer, more intense chocolate flavor. Just be mindful that it could make the cupcakes slightly less sweet, so adjust the sugar if you prefer a sweeter result.
Do I need to use paper liners for these cupcakes?
Paper liners make it easier to remove the cupcakes and clean up afterward, but if you prefer, you can grease the muffin pan well and bake them without liners. Just handle them carefully when removing to keep the cheesecake filling intact.
Why is my cheesecake filling runny?
If your cheesecake filling is too loose, it might be under-beaten or too warm. Make sure your cream cheese is at room temperature but not melted, and beat until smooth but firm. Refrigerating your filling briefly before assembling can also help.
Can I double the recipe?
Yes, this recipe scales well. Just be sure to bake the cupcakes in batches if your oven can’t hold more at once, and watch the baking time carefully, as it may vary slightly with a larger quantity.
Final Thoughts
Once you try this Cheesecake Stuffed Chocolate Cupcakes Recipe, it’s likely to become one of your go-to desserts for any occasion that calls for something special. The dreamy cheesecake center paired with rich chocolate cupcake is simply unforgettable. I encourage you to dive headfirst into this recipe—you’ll find the process fun, the results impressive, and the taste absolutely to die for. Happy baking and even happier indulging!
Print
Cheesecake Stuffed Chocolate Cupcakes Recipe
- Prep Time: 15 minutes
- Cook Time: 25 minutes
- Total Time: 40 minutes
- Yield: 16 servings
- Category: Dessert
- Method: Baking
- Cuisine: American
Description
These Cheesecake Stuffed Chocolate Cupcakes combine rich, fudgy chocolate cupcakes with a creamy, luscious cheesecake center, topped with melted chocolate chips for an irresistible treat. Perfect for dessert lovers who enjoy a delightful surprise inside their cupcakes.
Ingredients
Chocolate Cupcakes 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 the oven: Preheat your oven to 350°F (175°C). Line two muffin tins with 16 paper liners to prepare for baking.
- Melt chocolate: In the microwave, melt 1/2 cup of the semisweet chocolate chips. Allow the melted chocolate to cool slightly before using it in the batter.
- Prepare dry and wet ingredients: In a bowl, mix together the all-purpose flour, baking soda, and salt. In a separate bowl, whisk together the granulated sugar, vegetable oil, egg, and vanilla extract. Gradually add the melted chocolate and water alternately with the dry flour mixture into the wet ingredients, stirring until combined. The batter will be thin.
- Make cheesecake filling: Using a mixer, beat the cream cheese, granulated sugar, egg, and salt together until smooth and creamy. Fold in 1 cup of the remaining semisweet chocolate chips into the cheesecake mixture.
- Assemble cupcakes: Fill each lined muffin cup halfway with the chocolate batter. Add about 1 tablespoon of the cheesecake filling on top of the batter, then cover with the remaining chocolate batter to fill the cups.
- Bake: Bake the cupcakes for 20-25 minutes until they are set and a toothpick inserted near the edge comes out clean. Immediately after removing from the oven, sprinkle the remaining chocolate chips on top while they are still hot so they melt and create a glossy chocolate frosting.
- Cool: Allow the cupcakes to cool in the pan for a few minutes, then transfer them to a wire rack to cool completely before serving.
Notes
- Ensure the cream cheese is at room temperature to achieve a smooth cheesecake filling.
- The batter will be thin; this is normal and will result in moist cupcakes.
- You can substitute vegetable oil with canola oil or melted butter if preferred.
- For a richer chocolate flavor, use high-quality semisweet chocolate chips.
- Store cupcakes in an airtight container in the refrigerator due to the cream cheese filling, and consume within 3-4 days.

