Get ready to fall in love with the ultimate autumn dessert: our incredible Pumpkin Cheesecake Muffins. Imagine a perfectly spiced, moist pumpkin muffin with a luscious, creamy cheesecake filling swirled right in. It’s the best of both worlds in one perfect, handheld treat. Whether you’re looking for a special breakfast, an afternoon snack, or a crowd-pleasing dessert, this recipe is your answer. These muffins are surprisingly simple to make and deliver that cozy, comforting flavor everyone craves when the leaves start to turn.

Why You’ll Love These Pumpkin Cheesecake Muffins
If you’re a fan of fall flavors, this recipe is a must-try. Each bite is a delightful combination of textures and tastes, from the tender pumpkin-spiced cake to the rich, tangy cream cheese swirl. They look impressive enough for a special occasion but are easy enough for a spontaneous weekend baking session.
- Perfectly Spiced: A warm blend of cinnamon, nutmeg, and allspice gives these muffins that classic pumpkin spice flavor.
- Creamy Cheesecake Swirl: The smooth, tangy cream cheese filling perfectly complements the warm spices of the muffin.
- Incredibly Moist: Thanks to the pumpkin puree, these muffins stay moist and tender for days.
- Easy to Make: With simple steps and common ingredients, this recipe is accessible even for beginner bakers.
Key Ingredients You’ll Need
To create these delicious muffins, we’ll be making two separate components: the muffin batter and the cheesecake filling. Here’s what you’ll need for each.

For the Pumpkin Muffins
- All-Purpose Flour: Provides the structure for our muffins.
- Granulated & Brown Sugar: A mix of both gives the perfect balance of sweetness and moisture.
- Baking Soda: Our leavening agent to help the muffins rise.
- Spices: A classic autumn blend of ground cinnamon, nutmeg, and allspice.
- Salt: Enhances all the other flavors.
- Pumpkin Puree: Use 100% pure pumpkin puree, not pumpkin pie filling.
- Eggs: To bind the ingredients together.
- Vegetable Oil: Ensures a super moist muffin crumb.
- Vanilla Extract: Adds a touch of warmth and flavor.
For the Cheesecake Filling
- Cream Cheese: Use full-fat, block-style cream cheese, softened to room temperature for a smooth, lump-free filling.
- Granulated Sugar: For sweetness.
- Egg Yolk: Adds richness and helps the filling set.
- Vanilla Extract: Complements the pumpkin spice flavors beautifully.
How to Make Pumpkin Cheesecake Muffins (Step-by-Step)
Follow these simple steps to create the most delicious pumpkin cream cheese muffins right in your own kitchen. It’s as easy as mixing, layering, and baking!
Step 1: Prep Your Muffin Tin and Oven
First, preheat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners. Getting your station ready first makes the entire process smooth and seamless.
Step 2: Make the Cheesecake Filling
In a medium bowl, beat the softened cream cheese and granulated sugar together with an electric mixer until smooth and creamy. Beat in the egg yolk and vanilla extract until just combined. Be careful not to overmix. Set this aside while you prepare the muffin batter.
Step 3: Mix the Muffin Batter
In a large bowl, whisk together the all-purpose flour, granulated sugar, brown sugar, baking soda, cinnamon, nutmeg, allspice, and salt. In a separate bowl, whisk together the pumpkin puree, eggs, vegetable oil, and vanilla extract. Pour the wet ingredients into the dry ingredients and stir until just combined. Do not overmix the batter; a few lumps are perfectly fine.
Step 4: Assemble and Bake
Fill each muffin liner about two-thirds full with the pumpkin batter. Then, top each muffin with a generous dollop (about 1 tablespoon) of the cream cheese filling. Use a toothpick or a small knife to gently swirl the cheesecake filling into the batter. Bake for 20-25 minutes, or until a toothpick inserted into the muffin part comes out clean. Let the muffins cool in the pan for a few minutes before transferring them to a wire rack to cool completely.
Pro Tips for Perfect Muffins Every Time
Want to ensure your Pumpkin Cheesecake Muffins turn out perfectly? Here are a few expert tips.
- Room Temperature Ingredients: For the smoothest cheesecake filling, make sure your cream cheese and egg are at room temperature.
- Don’t Overmix: Overmixing the muffin batter can lead to tough, dense muffins. Mix only until the flour is just incorporated.
- Use an Ice Cream Scoop: For evenly sized muffins, use a standard-size ice cream scoop to portion the batter into the liners.
Fun Variations to Try
While this recipe is fantastic as is, you can easily customize it! For a delightful crunch, try adding a cinnamon-pecan streusel topping before baking. You could also mix in chocolate chips into the pumpkin batter for a decadent twist. If you love cheesecakes, you might also enjoy our incredible burnt basque cheesecake loaf.
Storing and Freezing Instructions
Because of the cream cheese filling, these muffins should be stored in an airtight container in the refrigerator for up to 5 days. For longer storage, you can freeze them! Place the completely cooled muffins in a freezer-safe bag or container and freeze for up to 3 months. Thaw them in the refrigerator or at room temperature before enjoying.
Frequently Asked Questions
No, it is not recommended. Pumpkin pie filling is pre-sweetened and spiced, which will alter the flavor and sweetness of the muffins. Be sure to use 100% pure pumpkin puree for this recipe.
Yes, absolutely! Allow the muffins to cool completely, then place them in a freezer-safe bag or container. They can be frozen for up to 3 months. Thaw them in the refrigerator before serving.
After topping the batter with a dollop of the cheesecake filling, use a toothpick or the tip of a knife to make a gentle figure-eight motion. Don’t over-swirl, as that can cause the two mixtures to blend together too much.
Because of the cream cheese filling, these muffins must be stored in an airtight container in the refrigerator. They will stay fresh for up to 5 days.
The filling might sink if it’s too thin or if the muffin batter is too thick. Ensure your cream cheese is softened but not melted. Also, be careful not to overmix the filling, which can incorporate too much air.
More Delicious Recipes to Try
If you enjoyed these muffins, explore some of our other popular treats. For a decadent chocolate experience, try our famous s’mores cupcakes. Or, for a different autumn-inspired dessert, this pumpkin pecan cobbler is always a huge hit!
Ready to Bake? Let’s Go!
These Pumpkin Cheesecake Muffins are the perfect way to celebrate the flavors of fall. They are sure to become a new family favorite. If you make this recipe, we’d love to see it! Share your creations on Pinterest and leave a comment below to let us know how they turned out.

Pumpkin Cheesecake Muffins Recipe

Pumpkin Cheesecake Muffins: The Perfect Fall Treat
Ingredients
Equipment
Method
- Preheat oven to 375°F (190°C). Line a 12-cup standard muffin tin with paper liners.
- Make the cheesecake filling: In a medium bowl, beat the softened cream cheese and granulated sugar with an electric mixer on medium speed until smooth. Add the egg yolk and vanilla, and beat until just combined. Set aside.
- Make the muffin batter: In a large bowl, whisk together the flour, granulated sugar, brown sugar, baking soda, cinnamon, nutmeg, allspice, and salt.
- In a separate medium bowl, whisk together the pumpkin puree, eggs, vegetable oil, and vanilla extract until well combined.
- Pour the wet ingredients into the dry ingredients and stir with a rubber spatula until just combined. Do not overmix.
- Divide the pumpkin batter evenly among the 12 muffin cups, filling each about two-thirds full.
- Top each muffin with about 1 tablespoon of the cheesecake mixture. Use a toothpick or the tip of a knife to gently swirl the cheesecake filling into the pumpkin batter.
- Bake for 20-25 minutes, or until a toothpick inserted into the pumpkin muffin part comes out with moist crumbs attached. The cheesecake filling should be set.
- Let the muffins cool in the pan for 5-10 minutes before transferring them to a wire rack to cool completely.
Notes
Room Temperature Ingredients: For the smoothest filling, ensure your cream cheese and egg yolk are at room temperature before mixing.
Pumpkin Puree: Be sure to use 100% pure pumpkin puree, not pumpkin pie filling, which is already sweetened and spiced.




