Cheesecake Chocolate Cupcakes are packed with luscious chocolate and filled with a creamy, tangy surprise on the inside. These are not your average chocolate cupcakes.

Cupcakes can be so hit or miss. In most cases, they are completely dry and have an underwhelming dollop of whipped cream on top. Oftentimes, you can lick the whipped cream off the top and throw the cake portion to the side. Pretty disappointing if you ask me.
These cupcakes prevail against all odds due to one, shining star ingredient: cream cheese. Piped directly into the center of the cupcake, the cream cheese filling spread creates an unparalleled moistness and texture. Get ready to have all your notions of cupcakes be turned upside down.
Cheesecake Chocolate Cupcakes: The Low Down
- Flavor: It’s all about how the chocolate and cream cheese compliment one another. The cocoa powder makes the cake rich, the chocolate chips add the necessary texture, and the cream cheese ties everything together. The end result is a perfectly balanced cupcake that will have you questioning why you ever went the store bought route.
- Texture: The best cupcakes are dense, not airy. What sets this recipe apart from the rest is the moisture that gets locked into the batter.
- Time: No mixer required. This recipe comes together in a jiff and requires little to no baking expertise.
How to Make Cheesecake Chocolate Cupcakes
Despite how impressive they look, these cupcakes are super simple to make. Follow the instructions below to nail the recipe every time.
- Combine cream cheese, egg, and sugar until smooth.
- Stir in chocolate chips. Set aside.
- Combine flour, sugar, cocoa, baking soda, and salt. Mix in water, oil, and vinegar.
- Fill muffin cups halfway with batter. Top each with a dollop of the cream cheese mixture.
- Bake at 350°F for about 25 minutes. Cool for 5 minutes and place on wire rack.
- Combine cream cheese, butter, vanilla extract, and confectioners sugar until fluffy.
- Fill piping bag with mixture and top cupcakes as you wish.






Tips for the Best Chocolate Cupcakes
These cupcakes are undoubtedly easy, but follow the tips below to make them that much more full proof.
- Room temperature butter & cream cheese. Save your forearms the trouble and bring both the cream cheese and butter to room temperature for easy stirring.
- Don’t over fill. A small dollop goes a long way. Don’t over do it with the cream cheese filling, or risk misshapen cupcakes.
- Don’t over mix. Overmixing the batter can cause it to lose its signature fluffiness.
- Measuring matters. When it comes to baking, measuring matters. Do your due diligence and measure each ingredient carefully. This will make all the difference when it comes to texture and moistness.

Tips on Decorating Cupcakes
Now is the time to get creative. Follow the below tips to create cupcakes that look too pretty to eat.
- Pick the right tip. So many tips, so little time. Choose whichever piping tip you like.
- Wax on, wipe off. Don’t like your cupcake topping? Simply whip off the cream and start over again.
- Keep your cream cold. Store your cupcakes in the refrigerator to prevent the cream cheese topping from melting.


FAQ
What makes a cupcake moist and fluffy?
The white vinegar makes the cake super moist, but the cream cheese filling brings it home. The combination of the two will create the best texture possible.
Why do cupcakes shrink/sink after baking?
A high liquid content will make your cupcakes expand and shrink. Not to worry – this is a natural process and it means your cupcakes will turn out dense and luscious.
Can you freeze cheesecake cupcakes?
Absolutely! These cupcakes are perfect for freezing to enjoy later. When you’re ready to eat, allow them to thaw in the refrigerator overnight. Warm in the microwave for 30-45 seconds and enjoy.

More Chocolate Treats!
Are you a chocolate addict? Check out some of these other sweet treats!
- Chocolate Babka Recipe – Sweet, chocolatey bread. Best dunked in coffee for breakfast.
- Chocolate Salami – Yes, you read it right. This salami log is made out of chocolate and perfect for your next holiday tray.
- Chocolate Dipped Figs – It’s fig season, so why not dip this high-class fruit in chocolate?
- Chocolate Raspberry Truffles – Truffles at home — the easy way.
Recipe
Ingredients
Cupcake Dough
- 3 cup all-purpose flour
- 2 cup sugar
- 2/3 cup cocoa powder (unsweetened)
- 2 tsp baking soda
- 1 tsp salt
- 2 cup water
- 2/3 cup vegetable oil
- 2 tbsp white vinegar
- 2 tsp vanilla extract
Cupcale Frosting
- 16 oz cream cheese softened
- 8 tbsp unsalted butter softened
- 2 cup confectioners sugar
- 1 tsp vanilla extract
Instructions
Cupcake Filling
- Beat cream cheese, egg, and sugar in a bowl until fluffy.
- Mix in chocolate chips and set aside.
Cupcake
- Combine flour, sugar, cocoa, baking soda, and salt. Mix in water, oil, and vinegar in small portions.
- Fill muffin cups half full with batter. Top each cupcake with about 1 tablespoon of the cream cheese mixture.
- Bake at 350°F for about 25 minutes, or until a toothpick comes out clean. Cool for about 5 minutes before removing from the cupcake pan and placing on wire rack.
No eggs for this recipe?
Hi Danita, No eggs! Enjoy! 🙂
Hi there, the serving size says 30 units, which is a little confusing. Does that mean the recipe yields 30 cupcakes? Thank you!
Hi Virginia, Yes, it makes 30 cupcakes! Enjoy!
No eggs in the cake batter?
Hi there, there are eggs in the cream cheese mixture that you use. I hope this helps. Happy baking!
When making the filling, it ended up being too much like liquid. Can I still use it as filling?
Mine came out liquid too when I beat the cream cheese, egg, and sugar. Maybe we didn’t mix it long enough?
Hi Anastasiya, Hmm, perhaps the cream cheese was softened too much? The cream cheese should be softened at room temperature, but still cold. Beat it with the egg and sugar until fluffy- not too long. Hope you give it another try!
Hi Michelle, it should be pretty soft but not sure why it would turn into liquid. What type of cream cheese did you use?
Can I make the frosting ahead of time and how long does it keep in refrigerator in a nice sealed container.
Hey Mary, yes, that should work fine. Enjoy
Wow these were amazing and the tips really helped me be a success! I think I overmix, overfill and never soften butter and cream cheese! What a difference.
So glad you found the tips helpful 🙂
I think I have found my new favorite dessert! Holy cow, these cupcakes are the best thing!! The cheesecake middle takes them to a whole new level!
Haha, yes got you hooked!! Glad you enjoyed them 🙂
These chocolate cupcakes are truly amazing! The cupcake batter is so soft, fluffy, and moist. And the frosting is delicious! LOVE this recipe.
So glad you loved it, thank you for your feedback, Valentina 🙂
What is the purpose of the vinegar in this recipe?
It's there to dissolve the baking soda.
Best cupcakes evere? Super moist . Thank you for the recipe .
Yeyy, so happy you loved it. The cream cheese makes them so much better. 🙂
When I was making the cream cheese mixture that goes on top, no matter how long I was mixing it for, it was still lumpy. Any suggestions?
It might be the quality of cream cheese, what brand do you use? Was the butter at room temperature?
Best chocolate cupcake that I made and ever tasted! Definitely a keeper in my recipe book.
Thank you so much!
wow, I make the same cupcakes!!! aren't these great!
They are really good, creamy and so good 🙂
Natasha, does this recipe make 24 cup cakes?
It makes 30 cupcakes. I was making them a little smaller in size.