If you have a serious sweet tooth and love the idea of marrying two incredible desserts into one, you are going to adore this Cheesecake Stuffed Chocolate Muffins Recipe. Imagine tender, rich chocolate muffins with a luscious swirl of creamy cheesecake baked right inside. Each bite offers the perfect balance of dense cocoa flavor and smooth cheesecake tang, making these muffins a standout treat for breakfast, snack time, or dessert. Once you try this recipe, it’s hard not to keep coming back for more!

Ingredients You’ll Need
This Cheesecake Stuffed Chocolate Muffins Recipe calls for simple, everyday ingredients that come together to create something extraordinary. Every item is essential for building the perfect texture, taste, and chocolatey goodness that make these muffins irresistible.
- All-purpose flour: The foundation that provides structure and tenderness.
- Unsweetened cocoa powder: Adds rich chocolate intensity without overpowering sweetness.
- Baking soda: Gives the muffins a gentle lift for a soft crumb.
- Salt: Enhances the chocolate flavor and balances sweetness perfectly.
- Granulated sugar: Sweetens and helps create a tender bite.
- Brown sugar: Adds moisture and a subtle caramel depth.
- Vegetable oil: Keeps muffins moist and soft, better than butter for this recipe.
- Eggs: Bind ingredients and provide richness.
- Vanilla extract: Brings warmth and a delightful aroma.
- Buttermilk: Adds tanginess and helps keep the muffins tender.
- Mini chocolate chips: Sprinkle throughout for little pockets of melty chocolate.
- Cream cheese (for filling): Creates that irresistible cheesecake center.
- Sugar (for filling): Sweetens the cheesecake filling just right.
- Egg yolk (for filling): Adds richness and helps set the filling.
- Vanilla extract (for filling): Enhances the creamy cheesecake flavor.
How to Make Cheesecake Stuffed Chocolate Muffins Recipe
Step 1: Prepare Your Batter
Start by preheating your oven to 350°F and lining a muffin tin with paper liners to prevent sticking. Whisk together the dry ingredients — flour, cocoa powder, baking soda, and salt — in a bowl. In a separate large bowl, beat your sugars, oil, eggs, and vanilla until everything is smooth and homogenous. Gradually add the dry ingredients to the wet, stirring just until combined to keep your muffins tender. Finally, fold in the buttermilk and mini chocolate chips for that dreamy chocolate burst in every bite.
Step 2: Mix the Cheesecake Filling
While the main batter rests, whip up the cheesecake filling in another bowl. Combine softened cream cheese, sugar, egg yolk, and vanilla extract, mixing until smooth and creamy. This filling will add that dreamy gooey center that makes these muffins unforgettable.
Step 3: Assemble the Muffins
Fill each muffin liner about one-third full with the chocolate batter. Add a generous spoonful of cheesecake filling right in the center of each muffin. Then, cover with more chocolate batter to seal in that creamy surprise. This layering technique ensures every muffin bursts with cheesecake in each bite.
Step 4: Bake to Perfection
Bake the muffins for 18 to 22 minutes, or until the tops are set and a toothpick inserted near the edge comes out clean. Let them cool in the pan for 5 minutes before transferring to a wire rack to cool completely — warming or room temperature serve best to enjoy that melty cheesecake center.
How to Serve Cheesecake Stuffed Chocolate Muffins Recipe

Garnishes
For an extra indulgent touch, sprinkle a few extra mini chocolate chips or a light dusting of powdered sugar on top before serving. Fresh berries or a drizzle of chocolate ganache also pair beautifully, adding a little elegance and freshness to these cozy treats.
Side Dishes
These muffins shine on their own but also make a fantastic partner for a creamy latte, a cold glass of milk, or even a scoop of vanilla ice cream for a decadent dessert duo. If you want to keep it simple yet satisfying, a spoonful of whipped cream alongside works wonders too.
Creative Ways to Present
Turn these into a fun brunch feature by slicing the muffin in half and adding fresh fruit or berry compote. You can also serve them warm with a small dish of cream cheese frosting for dipping. For celebrations, place them in pretty cupcake wrappers and stack on a tiered platter to impress your guests effortlessly.
Make Ahead and Storage
Storing Leftovers
You can keep leftover muffins fresh by storing them in an airtight container in the refrigerator for up to five days. This helps preserve the moisture of both the chocolate muffin and the cheesecake filling, so they’re just as delicious when enjoyed later.
Freezing
These muffins freeze beautifully! Wrap each muffin individually in plastic wrap or foil, then place them in a freezer-safe bag or container. They will keep their flavor and texture for up to two months, making them an excellent make-ahead treat for busy days or unexpected guests.
Reheating
To enjoy frozen muffins, simply thaw at room temperature, then warm them gently in the microwave for about 15-20 seconds or in a low oven to revive that soft, fresh-baked texture. Just avoid overheating so the cheesecake filling remains luxuriously creamy.
FAQs
Can I use regular chocolate chips instead of mini ones?
Absolutely! Regular-sized chocolate chips work just fine, but mini chips distribute more evenly throughout the batter and melt slightly faster, which creates those delightful little pockets of gooey chocolate.
Is it necessary to chill the cream cheese before mixing the filling?
It’s best to use softened cream cheese at room temperature. This ensures that the filling mixes smoothly without lumps. If the cream cheese is too cold, you might get an uneven texture in the cheesecake center.
Can I make these muffins dairy-free or vegan?
This recipe relies on cream cheese and eggs for the cheesecake filling, so it would require substitutions. There are dairy-free cream cheese alternatives and egg replacers available, but keep in mind texture and flavor may differ from the original.
How do I know when the muffins are done baking?
The muffin tops should feel set and bounce back lightly when touched. Inserting a toothpick near the edges (avoiding the cheesecake center) should come out clean or with just a few moist crumbs attached.
Can I add other mix-ins to the batter?
Definitely! Chopped nuts, dried cherries, or even a swirl of peanut butter can add exciting flavors and textures. Just be mindful not to overload the batter, so the muffins maintain their light, tender crumb.
Final Thoughts
If you’re looking for a dessert that’s both comforting and a little bit special, this Cheesecake Stuffed Chocolate Muffins Recipe is a must-try. It’s easy to make, impossible not to love, and perfect for sharing with friends and family. So preheat that oven and get ready for some seriously delicious moments!
Print
Cheesecake Stuffed Chocolate Muffins Recipe
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Total Time: 35 minutes
- Yield: 12 muffins
- Category: Dessert
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Description
These Cheesecake Stuffed Chocolate Muffins are a delightful treat combining rich chocolate batter with a creamy cheesecake filling. Perfect for dessert or a special snack, these muffins deliver a moist texture and a luscious surprise in the center, making them a crowd-pleaser for any occasion.
Ingredients
Chocolate Muffins:
- 1 cup all-purpose flour
- 1/2 cup unsweetened cocoa powder
- 1 teaspoon baking soda
- 1/4 teaspoon salt
- 1/2 cup granulated sugar
- 1/2 cup brown sugar
- 1/2 cup vegetable oil
- 2 large eggs
- 1 teaspoon vanilla extract
- 1/2 cup buttermilk
- 1/2 cup mini chocolate chips
Cheesecake Filling:
- 6 ounces cream cheese (softened)
- 3 tablespoons granulated sugar
- 1 large egg yolk
- 1/2 teaspoon vanilla extract
Instructions
- Preheat and Prepare Pan: Preheat the oven to 350°F (175°C) and line a muffin pan with paper liners to ensure easy removal and cleanup.
- Mix Dry Ingredients: In a medium bowl, whisk together the all-purpose flour, unsweetened cocoa powder, baking soda, and salt to evenly distribute leavening and flavor components.
- Combine Wet Ingredients: In a large bowl, mix the granulated sugar, brown sugar, vegetable oil, eggs, and vanilla extract until the mixture is smooth and homogenous, creating a rich base for the batter.
- Incorporate Dry into Wet: Add the dry ingredient mixture to the wet ingredients, stirring gently until just combined to avoid overmixing and ensure tender muffins.
- Add Buttermilk and Chocolate Chips: Fold in the buttermilk and mini chocolate chips carefully until the batter becomes smooth, thick, and evenly studded with chocolate chips.
- Prepare Cheesecake Filling: In a separate bowl, beat the softened cream cheese with granulated sugar, egg yolk, and vanilla extract until the filling is smooth and creamy.
- Assemble Muffins: Spoon about one-third of the chocolate batter into each muffin liner, then add a generous spoonful of the cheesecake filling in the center. Cover the filling with the remaining chocolate batter to fully encase the cheesecake layer.
- Bake: Bake in the preheated oven for 18 to 22 minutes, or until the muffin tops are set and a toothpick inserted near the edge (not the center cheesecake) comes out clean.
- Cool and Serve: Let the muffins cool in the pan for 5 minutes before transferring them to a wire rack to cool completely. This prevents the cheesecake from sinking and ensures perfect texture.
Notes
- For extra indulgence, sprinkle additional mini chocolate chips on top of each muffin before baking.
- Store muffins in the refrigerator for up to 5 days to maintain freshness and texture.
- For longer storage, freeze muffins and thaw at room temperature before serving.
- These muffins are best served at room temperature, allowing the cheesecake filling to be soft and creamy.

