Fall Pumpkin Cheesecake Muffins Recipe
Bake delicious pumpkin cheesecake muffins! Get our easy recipe for moist, spiced muffins with a creamy cheesecake swirl, perfect for fall.
These incredibly moist and creamy pumpkin cheesecake muffins combine the warm spices of fall with rich, tangy cheesecake swirls in every bite. Perfect for breakfast, dessert, or afternoon snacks, these bakery-style muffins are surprisingly simple to make at home.
Just like our popular cinnamon roll muffins, these treats disappear quickly from the kitchen counter, making them ideal for family gatherings and cozy autumn mornings.
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What Are Pumpkin Cheesecake Muffins?
Ever wondered why we call them “cheesecake” muffins when they’re clearly not cake? These delightful treats earned their name from the luscious cream cheese swirl that creates that signature cheesecake flavor throughout each fluffy muffin.
It’s like having your cake and eating your muffin too! After all, the way to a family’s heart is through their stomach, and these beauties never fail to impress. Ready to fall in love with your new favorite autumn treat?

Why You’ll Love This Pumpkin Cheesecake Muffins Recipe
The star of these muffins is undoubtedly the perfect marriage between spiced pumpkin batter and creamy cheesecake swirls. Each bite delivers warm cinnamon, nutmeg, and ginger notes balanced by the rich, tangy cream cheese mixture that melts in your mouth.
Making these at home saves you significant money compared to bakery prices while allowing you to control every ingredient. You’ll spend less than half what premium bakeries charge for similar muffins, and yours will be fresher and more flavorful.
The combination of pumpkin puree, cream cheese, and warming spices creates an irresistible aroma that fills your kitchen with the essence of fall. The tender crumb texture paired with the smooth cheesecake swirl makes each muffin feel like a special occasion treat.
Similar to our beloved apple cinnamon muffins, these pumpkin cheesecake muffins versions offer that same comforting, homemade goodness that brings families together. Why not surprise your loved ones this weekend with a batch of these incredible muffins?
How to Make Pumpkin Cheesecake Muffins
Quick Overview
These pumpkin cheesecake muffins are surprisingly easy to prepare, requiring just basic baking skills and common ingredients. The secret lies in creating two separate mixtures – a spiced pumpkin batter and a smooth cream cheese mixture – then swirling them together for that signature marbled effect.
Total Time: 45 minutes
- Prep Time: 15 minutes
- Bake Time: 22-25 minutes
- Cool Time: 5 minutes
- Yield: 12 standard muffins
Key Ingredients for Pumpkin Cheesecake Muffins
For the Pumpkin Muffin Base:
- 1¾ cups all-purpose flour
- 1 cup granulated sugar
- 1 teaspoon baking soda
- ½ teaspoon salt
- 1 teaspoon ground cinnamon
- ½ teaspoon ground nutmeg
- ¼ teaspoon ground ginger
- ¼ teaspoon ground cloves
- ⅓ cup vegetable oil
- 2 large eggs
- 1 cup pumpkin puree (not pumpkin pie filling)
- ⅓ cup water
For the Cheesecake Swirl:
- 8 oz cream cheese, softened
- ¼ cup granulated sugar
- 1 large egg yolk
- ½ teaspoon vanilla extract

Step-by-Step Instructions
Preparing Your Kitchen
Preheat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease thoroughly with butter. This prevents sticking and ensures easy removal.
Making the Cheesecake Mixture
In a medium bowl, beat the softened cream cheese until smooth and creamy using an electric mixer. Add ¼ cup sugar, egg yolk, and vanilla extract. Beat until completely combined and no lumps remain. Set aside while you prepare the muffin batter.
Creating the Pumpkin Batter
In a large bowl, whisk together flour, 1 cup sugar, baking soda, salt, cinnamon, nutmeg, ginger, and cloves until well combined. Create a well in the center of the dry ingredients.
In a separate bowl, whisk together vegetable oil, eggs, pumpkin puree, and water until smooth. Pour the wet ingredients into the well of dry ingredients. Gently fold together until just combined – don’t overmix, as this can make muffins tough.
Assembling the Muffins
Fill each muffin cup about ⅔ full with pumpkin batter. Add a generous tablespoon of cheesecake mixture on top of each muffin. Using a toothpick or knife, gently swirl the cheesecake mixture into the pumpkin batter, creating a marbled pattern.
Baking to Perfection
Bake for 22-25 minutes, or until a toothpick inserted into the pumpkin portion (not the cheesecake swirl) comes out with just a few moist crumbs. The tops should be golden brown and spring back lightly when touched.
Cool in the pan for 5 minutes before transferring to a wire rack. This prevents the muffins from becoming soggy on the bottom.
What to Serve Pumpkin Cheesecake Muffins With
These versatile muffins pair beautifully with hot coffee, spiced chai tea, or warm apple cider for the ultimate fall experience. For breakfast, serve alongside scrambled eggs and crispy bacon to balance the sweetness.
Create an elegant dessert presentation by serving with a dollop of whipped cream and a drizzle of caramel sauce. Fresh berries like cranberries or raspberries add a tart contrast that complements the rich flavors perfectly.
For afternoon tea or brunch gatherings, arrange these muffins on a tiered stand with other fall treats like pumpkin bread and apple turnovers.
Top Tips for Perfecting Pumpkin Cheesecake Muffins
Room Temperature Ingredients Are Key
Ensure your cream cheese and eggs are at room temperature before beginning. This creates a smoother cheesecake mixture that blends seamlessly without lumps.
Don’t Overmix the Batter
Stir the pumpkin batter just until ingredients are combined. Overmixing develops gluten, resulting in dense, tough muffins instead of tender ones.
Perfect Your Swirl Technique
When creating the marbled effect, use gentle motions with your toothpick. Too much swirling can muddy the colors instead of creating distinct patterns.
Test for Doneness Carefully
Insert your toothpick into the pumpkin portion, not the cheesecake swirl, as the cream cheese will always appear slightly underdone even when properly baked.
Ingredient Substitutions
Replace vegetable oil with melted butter for richer flavor, or use applesauce for a lighter version. Greek yogurt can substitute half the oil for added protein and tang.

Storing and Reheating Tips
Store these muffins in an airtight container at room temperature for up to 3 days, or refrigerate for up to one week due to the cream cheese content. The flavors actually improve after the first day as they meld together.
For longer storage, wrap individual muffins in plastic wrap and freeze for up to 3 months. Thaw overnight in the refrigerator or at room temperature for 2 hours.
To reheat, warm in a 300°F oven for 5-8 minutes, or microwave for 20-30 seconds. Avoid overheating, as this can make the cheesecake portion runny.
Nutrition Information
Nutrient | Per Muffin |
---|---|
Calories | 285 |
Total Fat | 12g |
Saturated Fat | 5g |
Cholesterol | 65mg |
Sodium | 245mg |
Total Carbs | 42g |
Dietary Fiber | 2g |
Sugars | 28g |
Protein | 6g |
Vitamin A | 45% DV |
Frequently Asked Questions
Can I use pumpkin pie filling instead of pumpkin puree?
No, pumpkin pie filling contains added sugars and spices that will throw off the recipe’s balance. Always use plain pumpkin puree for best results.
Why did my cheesecake swirl sink to the bottom?
This usually happens when the cream cheese mixture is too thin or the muffin batter is too thick. Ensure your cream cheese is properly softened but not melted.
Can I make mini muffins with this recipe?
Yes! Use a mini muffin tin and reduce baking time to 12-15 minutes. This recipe makes approximately 24 mini muffins.
How do I know when the muffins are done?
The tops should be golden brown and spring back when lightly touched. A toothpick inserted into the pumpkin portion should come out with just a few moist crumbs.
Can I add chocolate chips or nuts?
Absolutely! Fold ½ cup of chocolate chips, chopped pecans, or walnuts into the pumpkin batter before assembling the muffins.
My muffins are dense – what went wrong?
Dense muffins usually result from overmixing the batter or using too much flour. Measure flour by spooning it into the cup and leveling off.
Extra Tips for Success
Consider these additional techniques to elevate your muffins even further. Using cake flour instead of all-purpose creates an even more tender crumb, while adding a tablespoon of sour cream to the pumpkin batter increases moisture and tang.
For extra flavor depth, toast your spices in a dry pan for 30 seconds before adding to the flour mixture. This releases their essential oils and creates more complex flavors.
Create different variations by adding orange zest to the cheesecake mixture, or incorporating maple syrup in place of some granulated sugar for deeper fall flavors.
Make these muffins special occasion-worthy by topping with a simple cream cheese glaze made from powdered sugar, cream cheese, and milk.