Chocolate Cream Cheese Cupcakes

Total Time:Prep: 20 min. Bake: 25 min. + cooling
Molly Allen

By Molly Allen

Recipe by Shirley Dunbar, Mojave, California

Tested by Taste of Home Test Kitchen

Updated on Sep. 15, 2025

These chocolate cream cheese cupcakes offer the best combination of flavors with a fudgy chocolate base and a dreamy center.

These chocolate cream cheese cupcakes feature rich, fudgy chocolate and a cream cheese filling. Like cream cheese brownies, these cupcakes have a combination of chocolate and tangy cream cheese to create the ultimate sweet. Sometimes called black-bottom cupcakes, the chocolate dessert recipe starts with a quick and easy brownie-like batter. The cupcakes are then filled with a cream cheese mixture dotted with chocolate chips and peanut butter chips before baking. They’re perfect for dessert at home, a party, a bake sale or a potluck treat.

Ingredients for Chocolate Cream Cheese Cupcakes

  • Cream cheese: Start with softened cream cheese for the smoothest results when mixing the cream cheese filling.
  • Granulated sugar: Granulated sugar is essential for the cream cheese filling and chocolate cupcakes.
  • Egg: An egg provides structure to the cream cheese filling.
  • Salt: Salt balances the sweetness in the filling and in the cupcake batter.
  • Chocolate chips and peanut butter chips: Fold semisweet chocolate chips and peanut butter chips into the cream cheese filling for a pop of salty-sweet flavor.
  • Canola oil: Canola oil creates a rich texture and adds moisture to the cupcakes. If you don’t have canola oil, use vegetable oil instead.
  • White vinegar: A small amount of vinegar boosts the chocolate flavor and helps create a delicate texture in the cupcake.
  • Vanilla extract: Just 1 teaspoon of vanilla extract enhances the flavor of any baked good.
  • All-purpose flour: Grab all-purpose flour from the pantry to incorporate into the cupcake batter. The flour provides structure and plays a role in the texture.
  • Baking cocoa: Baking cocoa, or cocoa powder, is the key base of chocolate flavor in these cupcakes.
  • Baking soda: Baking soda adds lift to the cupcakes.

Directions

Step 1: Prep the cream cheese filling

A mixing bowl with creamed butter, sugar, and an egg, next to a hand mixer with beaters and cracked eggshells on parchment paper, all on a marble countertop.
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In a large bowl, beat the cream cheese until fluffy. Beat in the sugar, egg and salt until smooth.

A mixing bowl with creamy batter, chocolate chips, and peanut butter chips being stirred with a gray spatula on a marble surface.
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Fold in the chocolate and peanut butter chips. Set the filling aside.

Step 2: Make the cupcake batter

Bowls on a marble surface containing flour and cocoa, sugar, a whisk, a glass of water, a small jar of oil, a dish of vanilla extract, and a bowl of water, arranged for baking preparation.
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Preheat the oven to 350°F. In a large bowl, beat the sugar, water, oil, vinegar and vanilla until well blended. In a separate bowl, combine the flour, baking cocoa, baking soda and salt.

A person pours a bowl of cocoa powder mixture into another bowl with chocolate batter, using an electric hand mixer on a marble countertop.
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Gradually beat the flour mixture into the sugar mixture and mix well.

Step 3: Assemble and bake

A hand pours chocolate cupcake batter from a measuring cup into paper liners arranged in a muffin tin on a marble countertop.
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Fill paper-lined muffin cups halfway full with the batter.

A hand uses a spoon to add a light-colored batter with chocolate chips into cupcake liners filled with a darker batter in a muffin tray. A bowl of chip-filled batter sits nearby on a marble countertop.
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Top each with about 2 tablespoons cream cheese filling. Bake the cupcakes for 25 to 30 minutes or until a toothpick inserted into the center of one cupcake comes out clean. Cool the cupcakes for 10 minutes before removing them from the pans and moving them to wire racks to cool completely.

Editor’s Tip: The filling will partially cover the tops of the cupcakes. Don’t be alarmed—it’s supposed to happen!

Chocolate cupcakes with creamy, cheesecake-like centers and chocolate chips are cooling on a wire rack, each in a white paper liner.
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Chocolate Cream Cheese Cupcake Variations

  • Try dark chocolate: Love dark chocolate instead of semisweet? Use dark chocolate chips in the filling. You could also use dark chocolate baking cocoa for a deep, rich flavor.
  • Skip the peanut butter: If you’re not a fan of peanut butter, you can omit the peanut butter chips. Alternatively, you can swap in other baking chips, such as white chocolate chips, butterscotch chips or even espresso chips.
  • Go for chocolate mint: Skip the peanut butter chips and use mint chips instead. In addition, add 1 teaspoon of mint extract to the cupcake batter.

How to Store Chocolate Cream Cheese Cupcakes

Because there’s dairy in the filling, chocolate cream cheese cupcakes should be refrigerated until serving. Store the cupcakes in an airtight container or zip-top bag to preserve their flavor and texture. They’ll last up to five days in the fridge.

Can you freeze chocolate cream cheese cupcakes?

You can certainly freeze cupcakes. Store the chocolate cream cheese cupcakes in an airtight container or a freezer bag. They can be kept in the freezer for up to two months, then thaw them in the refrigerator before enjoying.

Can you make chocolate cream cheese cupcakes ahead of time?

Chocolate cream cheese cupcakes are a wonderful make-ahead dessert. Prep the batter and filling up to one day in advance. Let both set out at room temperature for up to 30 minutes before assembling and baking the cupcakes. After baking, store the cupcakes in an airtight container.

Chocolate Cream Cheese Cupcake Tips

Chocolate cupcakes with creamy cheesecake filling and chocolate chips, some in white paper liners, one broken open to show the moist texture inside, all on a white surface.
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Can you make chocolate cream cheese cupcakes with a boxed brownie mix?

Need a shortcut? Make these quicker with a boxed brownie mix. Prep the filling and the boxed brownie batter. Then, assemble and bake as directed.

How do you make mini chocolate cream cheese cupcakes?

If you have a mini cupcake pan, make tiny, bite-sized chocolate cream cheese cupcakes. You’ll need to reduce the baking time.

How should you serve chocolate cream cheese cupcakes?

These filled cupcakes can be enjoyed either cold or at room temperature. Eat a cupcake on its own, or pair it with a glass of milk, tea or coffee. You can also create a more elaborate dessert, like an ice cream sundae, by pairing the cupcake with a scoop of your favorite ice cream in a bowl and topping it with a drizzle of caramel sauce and sprinkles.

Watch How to Make Cream Cheese Chocolate Cupcakes

TEST KITCHEN APPROVED

Cream Cheese Chocolate Cupcakes

Contest Winner
Yield:1-1/2 dozen
Prep:20 min
Cook:25 min

Ingredients

  • 1 package (8 ounces) cream cheese, softened
  • 1/3 cup sugar
  • 1 large egg
  • 1/8 teaspoon salt
  • 1 cup semisweet chocolate chips
  • 1 cup peanut butter chips
  • cupcakes:
    • 1 cup sugar
    • 1 cup water
    • 1/3 cup canola oil
    • 1 tablespoon white vinegar
    • 1 teaspoon vanilla extract
    • 1-1/2 cups all-purpose flour
    • 1/4 cup baking cocoa
    • 1 teaspoon baking soda
    • 1/2 teaspoon salt
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Directions

  1. In a large bowl, beat cream cheese until fluffy. Beat in the sugar, egg and salt until smooth. Fold in chocolate and peanut butter chips; set aside.
  2. For cupcakes, in a large bowl, beat the sugar, water, oil, vinegar and vanilla until well blended. In a large bowl, combine the flour, cocoa, baking soda and salt; gradually beat into sugar mixture and mix well.
  3. Fill paper-lined muffin cups half full with batter. Top each with about 2 tablespoons cream cheese mixture. Bake at 350° for 25-30 minutes or until a toothpick inserted into cupcake comes out clean. Cool for 10 minutes before removing from pans to wire racks to cool completely.
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Smooth cream cheese inside makes these cupcakes so rich. The classic combination of peanut butter and chocolate chips comes through in every yummy bite. You'll be asked to make them again and again. —Shirley Dunbar, Mojave, California
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