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Pumpkin cheesecake muffins are everything you crave in fall baking: warm spices, creamy centers, and a soft, tender crumb that makes each bite feel like a hug. These muffins are perfect for breakfast, dessert, or that cozy afternoon snack with a hot drink in hand. What sets them apart is the luscious cheesecake swirl tucked right inside each spiced muffin, delivering a delightful contrast of flavors and textures.

They carry the comforting essence of pumpkin pie but in a portable, no-fork-needed form. The aroma that fills your kitchen while they bake is reason enough to make them. But once you sink your teeth into that first bite, you’ll understand why these muffins deserve a permanent spot in your seasonal rotation.

Why You’ll Love This Pumpkin Cheesecake Muffins Recipe

If you love the balance of creamy and fluffy in one treat, this recipe delivers. These muffins are tender and moist thanks to pumpkin puree, while the cheesecake layer adds a smooth, tangy surprise that cuts through the sweetness. They’re also freezer-friendly and hold up beautifully for meal prep or holiday gatherings.

Plus, there’s no need for fancy equipment. Just a couple of bowls, a whisk, and a muffin tin are all you need to whip up these bakery-worthy delights. With cinnamon, nutmeg, and vanilla dancing in each bite, this recipe is one you’ll find yourself revisiting year after year.

What Kind of Pumpkin Should I Use?

You want to use plain canned pumpkin puree—not pumpkin pie filling. Pumpkin puree gives the muffins moisture and natural flavor without added spices or sweeteners, which allows you to control the taste. If you’re feeling adventurous, you can also use homemade pumpkin puree, but make sure it’s well-drained to avoid overly wet batter.

Ingredients for the Pumpkin Cheesecake Muffins

These muffins come together with a handful of pantry staples, and each ingredient plays a crucial role in building flavor and texture.

Pumpkin Puree brings moisture and that earthy, slightly sweet flavor we all associate with fall.

All-Purpose Flour provides structure and helps the muffins rise just right.

Granulated Sugar sweetens the batter and balances the tang of the cheesecake filling.

Brown Sugar adds depth and a hint of molasses flavor, perfect with pumpkin.

Vegetable Oil ensures a moist, tender crumb.

Eggs bind everything together and help the muffins puff up in the oven.

Vanilla Extract enhances all the warm spices and brings balance to the overall flavor.

Baking Soda acts as the leavening agent for a nice rise.

Salt sharpens the flavors and balances the sweetness.

Cinnamon and Nutmeg are essential for that signature spiced pumpkin flavor.

Cream Cheese is the heart of the cheesecake filling—smooth, creamy, and slightly tangy.

Powdered Sugar sweetens the cheesecake layer without being gritty.

How To Make the Pumpkin Cheesecake Muffins

Step 1: Prepare the Cheesecake Filling

In a small bowl, beat softened cream cheese with powdered sugar and a splash of vanilla extract until smooth. Set aside while you make the muffin batter.

Step 2: Mix the Dry Ingredients

In a large bowl, whisk together flour, baking soda, salt, cinnamon, and nutmeg. This will be your spiced flour mixture.

Step 3: Mix the Wet Ingredients

In another bowl, combine pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, and vanilla extract. Mix until smooth and fully blended.

Step 4: Combine and Fill

Gradually add the dry ingredients to the wet mixture, stirring just until combined. Don’t overmix to keep the muffins tender.

Spoon the pumpkin batter into lined or greased muffin tins, filling each about 3/4 full. Add a dollop of the cheesecake filling to the center of each muffin and swirl gently with a toothpick or knife.

Step 5: Bake and Cool

Bake in a preheated oven at 350°F (175°C) for 18 to 22 minutes, or until a toothpick inserted in the muffin (not the cheesecake center) comes out clean. Let them cool in the pan for a few minutes before transferring to a wire rack.

How to Serve and Store These Muffins

Pumpkin cheesecake muffins are delightful served warm or at room temperature. They pair beautifully with a hot chai latte, coffee, or spiced cider. This recipe makes about 12 muffins, making it perfect for small gatherings, lunchbox treats, or weekend baking.

Once cooled, store them in an airtight container in the fridge for up to 5 days. You can also freeze them for up to 3 months—just let them thaw overnight in the fridge and reheat gently if desired.

What to Serve With Pumpkin Cheesecake Muffins?

Spiced Chai Latte

The warm spices in chai complement the flavors of the muffins beautifully.

Greek Yogurt Parfait

A great way to add some protein and freshness to your breakfast spread.

Apple Cinnamon Compote

A sweet and tangy topping that adds another layer of fall flavor.

Maple Glazed Bacon

For a sweet and savory contrast, this combo never fails.

Warm Vanilla Custard

Serve the muffins with a spoonful of custard for a cozy dessert.

Hot Chocolate

Especially rich varieties pair well with the cheesecake swirl.

Scrambled Eggs with Herbs

To balance out a sweet breakfast or brunch.

Roasted Pears

Caramelized pears are a perfect seasonal side to make the muffin moment extra special.

Want More Muffin Ideas with a Twist?

If you’re into creative spins on muffins, check out these other flavorful ideas from Luna Meals:

• Small Batch Pistachio Cream Cinnamon Rolls
• Blueberry Cheesecake Heaven Rolls
• Easy Banana Cream Pie Recipe
• Hot Fudge Brownie Bread
• Reese’s Peanut Butter Banana Bread

Save This Recipe For Later

📌 Save this recipe to your Pinterest dessert board so you can come back to it any time.

And let me know in the comments how yours turned out. Did you add pecans or a streusel topping? Maybe a drizzle of caramel on top?

I love hearing how others make these recipes their own. Questions are welcome too—let’s help each other bake smarter.

Explore beautifully curated health-boosting drinks on Luna Meals on Pinterest and discover your new go-to for feeling great!

Conclusion

Pumpkin cheesecake muffins are the best of both worlds: a soft, pumpkin-spiced muffin and a creamy cheesecake center. With simple steps and classic ingredients, they’re a treat worth repeating through fall and beyond. Whether you serve them at a brunch, holiday spread, or cozy morning breakfast, one thing’s for sure—they won’t last long once served.

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