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Chocolate Cream Cheese Muffins

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Freshly baked chocolate cream cheese muffins are the ultimate comfort food. With a combination of rich chocolate and cheesecake filling, they’re sure to satisfy your cravings.

If it came down to choosing between chocolate and cheesecake, I would have a hard time. But now I don’t have to worry about choosing one dessert over the other, because these delectable muffins have both! 

close up of stacked chocolate cream cheese muffins with a bite from the top one.

Our scratch-made muffins feature a creamy cheesecake filling. And they’re very easy to make, much simpler than the traditional cheesecake.

Trust me, you’re going to have a hard time resisting tasty treats but you don’t have to deny yourself. You can serve these delectable muffins for breakfast, brunch, dessert or afternoon snack.

ingredients needed to make chocolate cheesecake muffins with text overlay.
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Ingredients Needed

For the muffins: 

  • vegetable oil 
  • granulated sugar 
  • buttermilk – if you don’t have buttermilk, you can combine regular milk with a tablespoon of lemon juice. Let it sit for 5 minutes before pouring it into the batter. 
  • egg – room temperature works best
  • vanilla extract
  • yogurt – plain or vanilla 
  • all-purpose flour  
  • cocoa powder 
  • baking soda
  • pinch of salt

Cream cheese filling: 

  • cream cheese – allow time for it to soften so it’s easier to mix in
  • granulated sugar 
  • yogurt – plain or vanilla
  • egg – room temperature
  • vanilla extract

How to Make the Best Chocolate Cheesecake Muffins

Grease the muffin pan and set aside. Preheat the oven to 350 degrees F.

Using a mixer, beat the oil, buttermilk, sugar, egg, vanilla, and yogurt in a large bowl until combined. 

Mix the dry ingredients together in a separate bowl. 

side by side images of wet and dry ingredients and muffin tin with whisk and ingredients added to mixing bowl with text overlay.

Gently stir the dry ingredients into the wet ingredients. 

Set the batter aside. 

To make the cheesecake filling: 

Beat the softened cream cheese and sugar together in a large bowl using an electric mixer until it’s fluffy. 

Stir in the vanilla, egg, and yogurt. 

two images of cream cheese and sugar in a bowl and egg added to cream cheese mixture with text overlay.

Assemble the chocolate cream cheese muffins: 

Scoop the chocolate muffin batter so each cup is filled half way. There will be extra batter – save it for later. 

Make a crater in the center of the chocolate batter, then spoon in the cheesecake filling so it goes down into the muffin batter. 

side by side images of muffin tins filled with batter and cheesecake filling added to muffin batter with text overlay.

Top each muffin with the remaining chocolate batter and use a toothpick or skewer to swirl the filling on top. 

side by side images of filled muffin tin and front view of chocolate cheesecake muffins out of pan with text overlay.

Bake for 25-28 minutes. Remove from the oven and allow the muffins to cool in the pan for 15-20 minutes before removing from the pan. 

Tips for Making 

  • Do not over mix the muffin batter. This will make them tough and dense instead of nice and fluffy. 
  • Use muffin liners for easier cleanup. 
  • When the cheesecake muffins come out of the oven, they may have a dome shape on top. As they cool they’ll sink back down. This happens because the weight of the cheesecake filling is settling. 
  • Chocolate cream cheese muffins are amazing when served warm. And equally amazing when served cold. Your choice, you can’t go wrong either way! 
close up of chocolate cream cheese muffins.

How to Store 

Keep leftover muffins in an airtight container in the fridge for up to 4 days. Do not store these muffins on the counter – the cheesecake filling will spoil if it isn’t refrigerated.

To freeze, place the muffins on a baking sheet and into the freezer until solid (about an hour or two). Then transfer muffins to a freezer bag.

If preferred, wrap muffins individually in plastic wrap so you don’t have to thaw them all at once. Thaw in the refrigerator overnight. 

**Save Chocolate Cream Cheese Muffins Recipe for Later**

chocolate cream cheese muffins stacked on top of each other with text overlay.

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close up of two chocolate cheesecake muffins

Chocolate Cream Cheese Muffins

Freshly baked chocolate cream cheese muffins are the ultimate comfort food. With a combination of rich chocolate and cheesecake flavor, they're sure to satisfy your cravings.
4.75 from 4 votes
Print Pin Rate
Course: Breakfast, Dessert, Snack
Cuisine: American
Prep Time: 30 minutes
Cook Time: 25 minutes
Cooling: 15 minutes
Total Time: 1 hour 10 minutes
Servings: 12
Calories: 245kcal
Author: Lori


Chocolate muffins:

  • cup vegetable oil
  • cup granulated sugar
  • ¼ cup buttermilk
  • 1 egg, room temperature
  • 1 teaspoon vanilla extract
  • cup yogurt – plain or vanilla
  • 1 cup all-purpose flour
  • ¼ cup cocoa powder
  • ¾ teaspoon baking soda
  • pinch of salt

Cheesecake filling:

  • 8 ounces cream cheese, softened
  • 5 tablespoons granulated sugar
  • 2 tablespoons yogurt
  • 1 egg, room temperature
  • 1 teaspoon vanilla extract


  • Preheat the oven to 350 °F. Lightly grease a muffin pan and set aside.
  • In a large bowl, beat together oil, sugar, buttermilk, egg, vanilla extract, and yogurt until everything is well incorporated.
  • In second bowl mix the dry ingredients (flour, cocoa powder, baking soda, and salt).
  • Add the dry ingredients to the wet mixture and stir just until lightly combined. Set the batter aside and prepare the cream cheese filling.

Cream cheese filling

  • Using an electric mixer, beat softened cream cheese and sugar together in a large bowl until soft and creamy.
  • Add the yogurt, vanilla, and egg and mix until it’s smooth and well combined.


  • Scoop the chocolate muffin batter into the greased muffin tray, filling halfway. You’ll have a little extra batter – set it aside for later.
  • Evenly divide the cheesecake filling between the muffins. To set the cheesecake filling deep into the muffin batter, make a crater in the center of the batter with a spoon then add the cream cheese filling.
  • Spoon the remaining chocolate muffin batter on the top of the cheesecake filling. Use a toothpick, skewer or spoon to make swirls on top of the batter.
  • Bake for 25-28 minutes or until a toothpick inserted in the middle comes out clean with a few moist crumbs. Remove from oven and allow to cool in the pan for 15-20 minutes before removing muffins from pan.


  • Don’t overmix the muffin batter, stir just until combined.
  • Use muffin liners for easier cleanup.
  • The muffins will be domed when they come out of the oven and may sink a bit while cooling.
  • Muffins can be served warm or cold.
  • Store leftover muffins in an airtight container in the refrigerator for 3-4 days.
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Nutritional Estimate

Serving: 1muffin | Calories: 245kcal | Carbohydrates: 27g | Protein: 4g | Fat: 14g | Saturated Fat: 5g | Polyunsaturated Fat: 4g | Monounsaturated Fat: 4g | Trans Fat: 0.04g | Cholesterol: 48mg | Sodium: 149mg | Potassium: 97mg | Fiber: 1g | Sugar: 18g | Vitamin A: 312IU | Vitamin C: 0.1mg | Calcium: 45mg | Iron: 1mg

Nutritional information is provided as a reference, using an online calculator. We recommend verifying the information independently for accuracy.

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