Chocolate Cheesecake Muffins

Some days ask for more than a sweet snack. They call for something that feels like dessert, even when it fits in your hand. That’s what these mini chocolate cheesecakes deliver. They bake up like chocolate cream cheese cupcakes but bite like a brownie with a cheesecake center.

You’ll learn how to make a chocolate cheesecake recipe that’s easy, uses simple ingredients, and comes together in under an hour. These are chocolate muffin style, but with the surprise of cream cheese in the middle. No mixer required. No water bath. Just stir, spoon, and bake.

This recipe has a small detail that gives the chocolate a rich, deep flavor and helps the muffins stay moist. I’ll share it soon, but first, let’s walk through the steps that make these chocolate cheesecake cupcakes stand out.

Moist Chocolate Muffins with Cheesecake Centers

These muffins are soft, dense, and filled with smooth cheesecake. If you’ve ever had pumpkin cheesecake muffins in the fall, this version brings that same contrast between cake and cream, but with bold chocolate.

The muffin base is simple. Just flour, cocoa, sugar, and a few basics you likely already have in your pantry. You won’t need butter for this one. The fat comes from oil, which keeps the texture soft for days without drying out. The flavor, though, comes from something else entirely. We’ll get to that.

Start With the Cream Cheese Filling

The first step is mixing the cheesecake layer. I always start here so it’s ready to go once the batter comes together. Softened cream cheese, one egg yolk, vanilla, and sugar. Stir until smooth. That’s it. It should look like spreadable frosting, not whipped cream. Then it sits on the counter while you mix the muffin base.

Make the Chocolate Muffin Batter

For the batter, combine flour, unsweetened cocoa powder, baking soda, and a pinch of salt. I use regular all-purpose flour and a cocoa powder that isn’t too dark. I want that rich flavor without turning the muffins bitter.

In a second bowl, whisk the wet ingredients. This includes milk, oil, egg, sugar, and vanilla. Then melt chocolate chips and stir them in. This is the move that takes these from good to deep chocolate muffin territory. That melted chocolate thickens the batter and gives it a brownie-like texture once baked. If I feel like deepening the chocolate flavor, I stir in a teaspoon of espresso powder. It’s optional but always worth it.

Combine Gently, Bake With Confidence

I pour the wet mixture into the dry bowl and stir just enough to combine. Never overmix. If the batter still has a few streaks or small lumps, that’s fine. That’s how it should be.

To fill the muffin tin, I start with a spoonful of batter in each liner. Then I add a scoop of the cheesecake mix right in the center. I top it with more chocolate batter. You can leave the layers as they are or swirl the tops lightly with a toothpick.

Using every other cup in the muffin tin allows the muffins to rise taller and bake more evenly. This trick makes a real difference if you like that chocolate donut muffin look with domed tops and soft centers.

Bake and Test for Doneness

Bake at 350°F for 22 to 25 minutes. The tops will look set but still soft. I test for doneness by poking the outer edge of a muffin with a toothpick. The centers should remain a little creamy. That’s what gives them the texture of brownie cheesecake bites.

Let them cool in the tin for ten minutes, then transfer to a wire rack. I like to eat one warm while the chocolate is still melty. They keep well at room temperature for two days or in the fridge for five. You can also freeze them, which I’ve done more than once when I made a double batch.

Chocolate Muffins Moist or Dense? Let’s Talk Oil vs Butter

You might wonder why this recipe calls for oil instead of butter. I’ve tested both, and oil makes the texture softer and helps these mini chocolate muffins stay moist longer. Butter gives more flavor but leads to a tighter crumb.

In my notebook, the batches with oil always turned out taller and softer the next day. If you want to serve them the same day you bake, you can try butter. But for muffins that hold their texture and stay soft even after chilling, oil is the better choice.

One Muffin, One Paw, One Curious Cat

My cat Whiskers once got to a cooling rack of these muffins before I did. He didn’t eat them, but he pawed one clean off the counter. I took that as a warning. Now I guard them until they’re cool and safe in a container. Apparently, even the smell convinces him they’re more than just another cupcake.

The Secret That Makes Them Better Than a Regular Chocolate Cupcake

Here’s what I hinted at earlier. The melted chocolate chips make all the difference. Most chocolate muffin recipes skip this step and only use cocoa powder. But adding melted chocolate thickens the batter and gives the baked muffin that brownie chew you won’t get from cocoa alone.

That one move is the reason these land closer to chocolate cheesecake cupcakes or brownie cheesecake bites than plain muffins. Every time I skip it, the result feels flatter. When I include it, someone always asks me for the recipe.

What to Bake After These Chocolate Cheesecake Cupcakes

If you loved these, you might want to try other desserts with rich chocolate flavor or creamy centers. The Wacky Cake has no eggs or milk but tastes like it does. These Easy Brownies from Scratch come together fast and work every time.

If you like molten centers, try the Pistachio Chocolate Lava Cakes. For big family gatherings, the Texas Sheet Cake has a crowd-pleasing texture and rich frosting.

And if you’re in a no-bake mood, the Peanut Butter Dip pairs well with graham crackers or apple slices.

Save This Mini Cheesecake Muffin Recipe and Join the Conversation

Pin this chocolate muffin recipe to your board so you can find it fast the next time you need a dessert that looks more effort than it takes. These double as chocolate cheesecake cupcakes or mini chocolate cheesecakes depending on how you serve them.

Let me know in the comments if you tried the espresso twist or skipped the swirl. Did your cat swipe one like Whiskers did? I’d love to hear how yours turned out.

Continue to Content

Yield: 12 muffins

Chocolate Cheesecake Muffins Recipe

No Ratings

Print

Chocolate cheesecake muffins combine a rich, brownie-like chocolate batter with a smooth cream cheese center. These muffins are easy to make with simple ingredients and deliver a satisfying texture contrast in every bite. They bake up soft with a marbled top and creamy interior, perfect for casual desserts or a weekend treat.

Prep Time 20 minutes

Cook Time 25 minutes

Total Time 45 minutes

Ingredients

• for the cheesecake filling
• 8 oz (225g) full-fat cream cheese, softened
• 1/4 cup (50g) granulated sugar
• 1 large egg yolk
• 1/2 teaspoon vanilla extract~
• for the chocolate muffin batter
• 1 cup (125g) all-purpose flour
• 1/2 teaspoon baking soda
• 1/4 teaspoon salt
• 1/3 cup (30g) unsweetened cocoa powder
• 1/2 cup (100g) granulated sugar
• 1/2 cup (120ml) milk
• 1/3 cup (80ml) vegetable oil
• 1 teaspoon vanilla extract
• 1 large egg
• 1/2 cup (90g) semi-sweet chocolate chips, melted
• (optional) 1 teaspoon instant espresso powder

Instructions

1. PREHEAT THE OVEN: Set your oven to 350°F (175°C) and line a standard 12-cup muffin pan with paper liners. For taller muffins, use every other cavity in the tin to allow better air circulation.
2. MAKE THE CHEESECAKE FILLING: In a medium bowl, beat the cream cheese until smooth. Add the sugar, egg yolk, and vanilla extract. Stir until the mixture is completely smooth and creamy, then set aside.
3. PREPARE THE DRY INGREDIENTS: In a large mixing bowl, whisk together the flour, baking soda, salt, and cocoa powder until evenly combined.
4. MIX THE WET INGREDIENTS: In a separate bowl, whisk together the sugar, milk, vegetable oil, vanilla, and egg until smooth. Melt the chocolate chips in the microwave in short intervals, stirring until fully melted, and stir the chocolate into the wet ingredients. Add espresso powder if using.
5. COMBINE WET AND DRY MIXTURES: Pour the wet mixture into the dry ingredients and stir gently just until combined. Do not overmix; the batter should look slightly lumpy but cohesive.
6. FILL THE MUFFIN CUPS: Spoon about 1 tablespoon of chocolate batter into each prepared muffin liner. Add a generous spoonful of cheesecake filling on top of the batter, then spoon more chocolate batter over the filling to cover it. You may leave the layers as-is or lightly swirl the tops with a toothpick.
7. BAKE THE MUFFINS: Place the muffin pan in the oven and bake for 22 to 25 minutes. Check for doneness by inserting a toothpick into the edge of a muffin; it should come out with moist crumbs but no raw batter. The centers will remain slightly soft.
8. COOL AND SERVE: Allow the muffins to cool in the pan for 10 minutes, then transfer them to a wire rack. Serve warm or at room temperature.

Notes

For best results, use full-fat cream cheese. Do not overmix the batters to maintain a soft texture. Muffins can be stored in an airtight container at room temperature for up to 2 days or refrigerated for up to 5 days. They also freeze well.

Nutrition Information:

Yield:

12

Serving Size:

1
Amount Per Serving: Calories: 207Total Fat: 13gSaturated Fat: 6gTrans Fat: 0gUnsaturated Fat: 5gCholesterol: 74mgSodium: 254mgCarbohydrates: 19gFiber: 1gSugar: 7gProtein: 5g