Cheesecake Stuffed Chocolate Cupcakes

It started on a rainy afternoon, one of those days when everything outside looks gray, and baking feels like the only good plan. I wasn’t aiming for anything complicated—just wanted something chocolatey, maybe with a twist. The idea of combining a cupcake with cheesecake sounded like the kind of comfort dessert you’d want with a cozy blanket and a mug of coffee.

I pulled ingredients from the pantry without much thought, but as the cupcakes baked and the sweet, warm scent filled the kitchen, it felt like the day had shifted. When I finally tried one, the combination of that moist chocolate cake and creamy, slightly tangy cheesecake center was just right—not too rich, not too sweet, just the kind of dessert that makes you pause mid-bite.

Since then, these cupcakes have made regular appearances in my kitchen. They’re simple enough for a weeknight treat but still feel like something special when shared with friends. You don’t need frosting, piping tips, or anything fancy—just a craving and a little time.

Short Description

Cheesecake Stuffed Chocolate Cupcakes are rich, moist chocolate cupcakes filled with a creamy cheesecake center and topped with a glossy layer of melted chocolate. Perfectly balanced and incredibly indulgent, they’re a decadent two-in-one dessert.

Key Ingredients

• 2 cups (340g) semisweet chocolate chips, divided
• 1 1/2 cups (187g) all-purpose flour
• 1 tsp baking soda
• 1/2 tsp salt
• 1/2 cup (100g) granulated sugar
• 1/3 cup (66g) vegetable oil
• 1 large egg
• 1 tsp vanilla extract
• 1 cup water

For the Cheesecake Filling:

• 6 oz (170g) cream cheese, room temperature
• 1/4 cup (50g) granulated sugar
• 1 large egg
• 1/8 tsp salt
• 1 cup semisweet chocolate chips

Tools Needed

• 2 muffin tins
• 16 paper cupcake liners
• 2 mixing bowls (medium & large)
• Hand mixer or stand mixer
• Whisk
• Rubber spatula
• Microwave-safe bowl
• Toothpick

Cooking Instructions

Step 1: Preheat the Oven
Preheat your oven to 350°F (175°C). Line two muffin tins with 16 cupcake liners.

Step 2: Melt Chocolate for the Batter
Place 1/2 cup of chocolate chips in a microwave-safe bowl. Heat for 45 seconds, stir, then microwave in 10-second bursts until fully melted and smooth. Set aside to cool slightly.

Step 3: Make the Cupcake Batter
In a medium bowl, whisk together flour, baking soda, and salt. In a large bowl, mix the sugar, vegetable oil, egg, and vanilla extract. Stir in the melted chocolate. Gradually add the dry mixture, alternating with the water. Mix until just combined—the batter will be thin.

Step 4: Make the Cheesecake Filling
In another bowl, beat the softened cream cheese, sugar, egg, and salt until smooth and creamy. Fold in 1 cup of chocolate chips.

Step 5: Assemble the Cupcakes
Spoon chocolate batter into each cupcake liner, filling halfway. Add about 1 tablespoon of cheesecake filling to the center of each, then cover with more chocolate batter to fill about 3/4 full.

Step 6: Bake the Cupcakes
Bake for 20–25 minutes, or until a toothpick inserted in the center comes out mostly clean. Let them cool in the pan for 5 minutes before transferring to a rack.

Step 7: Add Final Chocolate Topping
While the cupcakes are still warm, sprinkle the remaining 1/2 cup chocolate chips on top. Let sit for 5 minutes until shiny, then gently spread for a glossy finish.

Why You’ll Love This Recipe

– Rich and chocolatey, with a creamy surprise inside

– Perfect balance of sweetness and tanginess

– No frosting required—built-in cheesecake center does the work

– Great for make-ahead desserts

– Kid-friendly and crowd-pleasing

– Simple pantry ingredients

– Can be made gluten-free with 1:1 flour swap

Mistakes to Avoid & Solutions

Overmixing the batter: This can lead to tough cupcakes. Stir just until everything is combined.

Not softening the cream cheese: Cold cream cheese creates lumps. Let it sit at room temp for at least 30 minutes.

Filling the liners too high: Overfilled liners can overflow. Aim to fill each only 3/4 full after the filling is added.

Using warm melted chocolate: It may cook the egg when mixed. Always cool it slightly first.

Skipping the chocolate topping: It adds a rich finish—don’t miss this final step!

Serving and Pairing Suggestions

– Serve slightly warm with a scoop of vanilla ice cream

– Add fresh raspberries or strawberries on the side

– Perfect for dessert platters, tea parties, or after-dinner treats

– Pair with cold milk, espresso, or a creamy latte

– Serve on a cake stand or in cupcake boxes for gifting

Storage and Reheating Tips

Refrigerate: Store in an airtight container for up to 5 days.

Freeze: Freeze individually wrapped cupcakes (without chocolate topping) for up to 2 months.

Reheat: Microwave for 10–15 seconds to restore that soft, melty center.

Avoid soggy bottoms: Place a paper towel under the cupcakes in the container to absorb excess moisture.

FAQs

1. Can I use dark chocolate chips instead of semisweet?
Yes, dark chocolate will create a richer flavor—perfect if you prefer less sweetness.

2. Can I make these gluten-free?
Absolutely! Just swap the all-purpose flour for a 1:1 gluten-free baking mix.

3. Do these cupcakes need to be refrigerated?
Yes, because of the cheesecake filling, it’s safest to refrigerate any leftovers.

4. Can I skip the chocolate topping?
You can, but it adds a luxurious finish. If you prefer a lighter version, skip or dust with cocoa powder.

5. Why is my cheesecake filling sinking?
If the batter is too thin or the filling is too heavy, it may sink. Try thickening your batter slightly next time.

Tips & Tricks

– Let the cream cheese reach full room temperature for a smoother filling.

– Use a cookie scoop to portion the cheesecake evenly.

– If the tops crack, dust with powdered sugar for a pretty finish.

– Chill cupcakes for 1 hour before serving for a firmer center.

– Don’t overbake—start checking at 20 minutes to avoid dry cupcakes.

Recipe Variations

Peanut Butter Twist:
Swap 1/3 of the cheesecake filling with creamy peanut butter. Stir until smooth and use as the center layer.

Mint Chocolate Cheesecake:
Add 1/2 tsp peppermint extract to the cheesecake filling and use dark chocolate chips.

Mocha Version:
Replace 1/4 cup of water with brewed espresso. Add 1 tsp instant coffee granules to the batter for a deeper flavor.

Raspberry Swirl:
Swirl 1 tbsp raspberry jam into the cheesecake filling for a fruity twist before spooning over the chocolate batter.

Nut-Free Option:
Use allergy-safe chocolate chips like Enjoy Life. No nuts required for big flavor.

Final Thoughts

These cupcakes have a way of disappearing quickly, especially when left out on the counter. People seem surprised by that hidden center, then immediately ask for another. That’s the charm—they don’t scream for attention, but once you try one, they stick with you.

They also hold up well, which makes them great for packing into lunchboxes, giving as little thank-you gifts, or just storing in the fridge for whenever that chocolate craving hits. And if you’re someone who finds joy in desserts that feel thoughtful but don’t ask for perfection, this recipe fits right in.

It’s the kind of bake that comes together easily and brings a bit of calm with it. Sometimes, that’s all you need from a recipe—something that works, tastes amazing, and feels good to make.