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Black Bottom Cupcakes With Mini Chocolate Chips

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Rich, indulgent, and incredibly moist, this chocolate cupcake recipe is perfect for any occasion. The cupcakes have a fudgy chocolate base with a creamy chocolate chip cheesecake center, are easy to make, and are a hit at every gathering.

Group of black bottom cupcakes and mini chocolate chips on a light gray surface. this …

I have been making these chocolate cream cheese cupcakes since high school. It was one of my favorite recipes and one of the first cupcake recipes I baked. Mainly because it was an easy recipe and because they are delicious. Back then, I used a chocolate cake mix. I now know that homemade chocolate cupcakes taste so much better than boxed!

  • Prep Time: 15 minutes
  • Recommended Baking Time: 16 to 20 minutes
  • Rest Time: 5 minutes
  • Total Time: 36 minutes
  • Yields: 12 regular-size cupcakes
  • Prep Level: Beginner +
Close up of a black bottom cupcake in a baking pan.

Reasons to Love This Black Bottom Cupcake Recipe

Flavor Combination: Rich chocolate cupcakes with a cream cheese center perfectly combined for a delicious dessert.

Easy to Make: Made with simple ingredients and ready in about 45 minutes.

Great for All Occasions: Perfect for birthday parties, Valentine’s Day, or any special occasion.

What You Will Need To Make This Recipe

Various sizes of bowls with ingredients for cupcakes: flour, cocoa powder, sugar, mini chocolate chips, milk, vegetable oil, cream cheese, salt, white vinegar, baking soda, vanilla extract, and an egg. Items are on a light gray surface.

Ingredients

  • All-purpose flour
  • White sugar – granulated
  • Unsweetened cocoa powder
  • Baking soda
  • Salt
  • Whole milk
  • Vegetable oil
  • White vinegar – See Recipe Tips
  • Vanilla extract
  • Cream cheese – See Recipe Tips 
  • Large egg
  • Chocolate chips – See Recipe Tips

Helpful Tools and Equipment

  • Mixing bowls (3)
  • Measuring cups
  • Measuring spoons
  • Sifter
  • Rubber spatula
  • Whisk
  • Electric mixer (hand mixer or stand mixer)
  • 12-cup muffin tin or 2 6-cup  
  • Cookie scoop
  • Cupcake liners
  • Wire rack
  • Oven mitts

How To Make Black Bottom Cupcakes

There is a large white mixing bowl with a flour and dry cocoa mixture in it. There is a whisk resting in the bowl. There is a white cloth napkin and a sifter in the background. Items are on a light gray surface.
There is a white mixing bowl with a light yellow liquid mixture in it. There is a whisk resting in the bowl. There is a large white mixing bowl with a flour and dry cocoa mixture in it. Bowls are on a light gray surface.
There is a large white mixing bowl with a flour, dry cocoa, and liquid mixture in it. There is a whisk resting in the bowl. There is an empty white bowl and a white cloth napkin. Items are on a light gray surface.
There is a large white mixing bowl with a chocolate cupcake mixture in it. There is a whisk resting in the bowl. There is an empty white bowl and a white cloth napkin. Items are on a light gray surface.

Make the chocolate batter:

  • In a large bowl, sift the flour, 1/2 cup sugar, cocoa powder, baking soda, and 1/2 teaspoon salt.
  • In a medium bowl, add the milk, oil, vinegar, and vanilla extract. Whisk until blended.
  • Add the wet ingredients to the dry ingredients, and stir until the batter is smooth and well combined.
Large glass mixing bowl with an egg, cream cheese, and sugar in it. There is a metal measuring cup with mini chocolate chips and a white cloth napkin. Items are on a light gray surface.
There is a large clear glass mixing bowl with a light yellow batter in it. There is a hand-held mixer over the bowl. There is a metal measuring cup with mini chocolate chips in it and a white cloth napkin. Items are on a light gray surface.
There is a large clear glass mixing bowl with a light yellow batter in it. There is a mound of mini chocolate chips on top of the batter. There is a light gray rubber spatula laying next to the bowl. There is an empty metal measuring cup and a white cloth napkin. Items are on a light gray surface.
There is a large clear glass mixing bowl with a light yellow cake batter and mini chocolate chips in it. There is a light gray rubber spatula resting in it. There is an empty metal measuring cup and a white cloth napkin. Items are on a light gray surface.

Prepare the cream cheese filling:

  • In a separate bowl, combine the cream cheese, 1/3 cup sugar, egg, and a dash of salt. Beat until smooth.
  • Fold in the chocolate chips.
There are two cupcake pans with white liners and chocolate batter in them. In the background there is a large clear glass bowl with a cream cheese and chocolate chip mixture in it. There is a scoop utensil resting in the bowl. Items are on a light gray surface.
There are 2 six cup muffin pans with white liners. There is a combination of chocolate batter and a cream cheese with chocolate chips mixture in them. There is an empty owl with a scoop utensil in the background. Items are on a light gray surface.

Assemble the cupcakes:

  • Divide the chocolate cupcake batter evenly among the lined cupcake pans.
  • Spoon about 1 tablespoon of the cream cheese mixture into the middle of each cupcake.
There are 2 six cup muffin pans with white liners. There are baked cupcakes in them with a combination of chocolate batter and a cream cheese with chocolate chips. Pans are on a dark wire rack. Rack is on a light gray surface.
There are 2 six cup muffin pans with white liners. There are baked cupcakes in them with a combination of chocolate batter and a cream cheese with chocolate chips. Pans are on a dark wire rack. Rack is on a light gray surface.

Bake:

  • Place the muffin tin(s) in the preheated oven and bake until the chocolate cake portion is set and the creamy cheesecake filling is slightly golden.
Nine black bottom cupcakes on a black wire rack. Rack is on a light gray surface.

Cool and Serve:

  • Remove the pan from the oven and allow the cupcakes to cool in the pan for about 5 minutes, then transfer the cupcakes to a wire rack to cool completely.

See the recipe card below for complete measurements and baking time.

Recipe Tips

You can use mini chocolate chips or regular chocolate chips. I prefer the miniature chocolate chips, so each delicious bite is filled with chocolate chips. You can use any of your favorite chips, such as dark chocolate, milk chocolate, or semi-sweet.

Be sure to use full-fat cream cheese at room temperature. Cold cream cheese won’t mix well and tends to leave small lumps in the filling.

Don’t skip the vinegar. When white vinegar and baking soda are combined in the batter, it helps the cupcake batter rise, making for a moist, fluffy texture.

How To Store

Due to the cream cheese, you need to refrigerate the black bottom cupcakes. Store the cupcakes in an airtight container in the refrigerator for up to 5 days.

Group of black bottom cupcakes and mini chocolate chips on a light wood surface.

Frequently Asked Questions

What does sifting do for baking?

Sifting the flour mixture will make the cupcakes lighter and fluffier.

What can I substitute white vinegar with?

You can substitute lemon juice or apple cider vinegar for white vinegar. But be aware that the flavor may slightly change, although it’s a small amount and may not be noticeable. Use a 1:1 ratio when substituting.

Can I make these in advance?

Absolutely! These delicious black bottom cupcakes are perfect for making ahead since they stay moist and flavorful. Bake them a day or two before and refrigerate. Bring to room temperature for about 30 minutes before serving.

Are you looking for some great new recipes to try? 

Check out some of my favorite sweet treats recipes – Scottish Shortbread, Chocolate Chip Pecan Pie, Easy Bread Pudding with Rum Sauce, and Easy Churro Cheesecake Bars.

Yield: 12

Black Bottom Cupcakes With Mini Chocolate Chips

Group of black bottom cupcakes and mini chocolate chips on a light gray surface.

Rich, indulgent, and incredibly moist, this chocolate cupcake recipe is perfect for any occasion. The cupcakes have a fudgy chocolate base with a creamy chocolate chip cheesecake center.

Prep Time 15 minutes
Cook Time 16 minutes
Additional Time 5 minutes
Total Time 36 minutes

Ingredients

  • 1 cup flour
  • 1/2 cup white sugar for cake batter + 1/3 cup for cream cheese filling
  • 1/4 cup unsweetened cocoa powder
  • 3/4 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1/2 cup milk
  • 1/4 cup vegetable oil
  • 1/2 teaspoon white vinegar
  • 1 teaspoon vanilla extract
  • 8 ounces cream cheese - at room temperature
  • 1 large egg - at room temperature
  • 1/2 cup mini chocolate chips

Instructions

  1. Preheat the oven to 350°F (175°C).
  2. Line the cupcake pans with paper liners or grease the muffin cups.
  3.  In a large bowl, sift the flour, 1/2 cup sugar, cocoa powder, baking soda, and 1/2 teaspoon salt.
  4. In a medium bowl, add the milk, oil, vinegar, and vanilla extract. Whisk until blended.
  5. Add the wet ingredients to the dry ingredients. Whisk or stir until the batter is smooth and well combined.
  6. In a separate bowl, combine the cream cheese, 1/3 cup sugar, egg, and a dash of salt. Beat on medium speed until smooth. 
  7. Fold in the chocolate chips.
  8. Divide the chocolate cupcake batter evenly among the cupcake liners; each muffin cup should be about 2/3 full with batter.
  9. Use a cookie scoop or spoon and add about 1 tablespoon of the cream cheese mixture into the center of each cupcake.
  10. Place the muffin tin(s) in the preheated oven and bake for 16 to 20 minutes (depending on your oven) or until a wooden pick or cake tester is inserted into the chocolate cake and comes out clean, and the cream cheese filling is set.
  11. Remove the pan from the oven and allow the cupcakes to cool in the pan for about 5 minutes, then transfer the cupcakes to a wire rack to cool completely.

Notes

Helpful Tools and Equipment

  • Mixing bowls (3)
  • Measuring cups
  • Measuring spoons
  • Sifter
  • Rubber spatula
  • Whisk
  • Electric mixer (hand mixer or stand mixer)
  • 12-cup muffin tin or 2 6-cup  
  • Cookie scoop
  • Cupcake liners
  • Wire rack
  • Oven mitts

Recipe Tips

  • You can use mini chocolate chips or regular chocolate chips. I prefer the miniature chocolate chips, so each delicious bite is filled with chocolate chips. You can use any of your favorite chips, such as dark chocolate, milk chocolate, or semi-sweet.
  •  Be sure to use full-fat cream cheese at room temperature. Cold cream cheese won’t mix well and tends to leave small lumps in the filling.
  • Don't skip the vinegar. When white vinegar and baking soda are combined in the batter, it helps the cupcake batter rise, making for a moist, fluffy texture.

How To Store

Due to the cream cheese, you need to refrigerate the black bottom cupcakes. Store the cupcakes in an airtight container in the refrigerator for up to 5 days.

Nutrition Information:

Yield:

12

Serving Size:

1
Amount Per Serving: Calories: 256Total Fat: 16gSaturated Fat: 7gTrans Fat: 0gUnsaturated Fat: 8gCholesterol: 42mgSodium: 263mgCarbohydrates: 24gFiber: 1gSugar: 14gProtein: 4g

Did you make this recipe?

Please leave a comment on the blog or share a photo on Pinterest

© Laura @ Join me in the Kitchen
Cuisine: American / Category: Desserts

Paula

Sunday 12th of January 2025

These sound so good. Bookmarked so I can try later. Visiting today from SSPS 342 #153,154&155

Laura @ Join me in the Kitchen

Sunday 12th of January 2025

Hi Paula! Would love to know if you make them and how you like them. Let me know if you have any questions! Cheers, Laura

EsmeSalon

Friday 10th of January 2025

WOW, the black bottoms caught my attention, thank you for sharing and participating at SSPS 342. See you at #343

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