Pumpkin Cheesecake Muffins – A Cozy Fall Favorite with a Creamy Twist

Why You’ll Love This Recipe

Pumpkin Cheesecake Muffins are the perfect way to enjoy the flavors of fall in a handheld treat. These moist, spiced pumpkin muffins are swirled with a luscious cream cheese filling, creating the ideal balance of warm autumn spices and tangy creaminess. Each bite delivers a little bit of everything—soft muffin, creamy cheesecake, and a hint of sweetness that makes them utterly irresistible.

They’re a wonderful option for breakfast, brunch, or dessert, and they pair beautifully with a cup of coffee or tea. Unlike a full cheesecake, these muffins are portable, easy to serve, and require less baking time. Whether you’re preparing a festive holiday spread or simply craving a seasonal treat, Pumpkin Cheesecake Muffins are a crowd-pleasing recipe that feels indulgent yet approachable.

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Ingredients

(Tip: You can find the complete list of ingredients and their measurements in the recipe card below.)

All-purpose flour – Forms the base of the muffins, giving them structure while keeping them tender.

Pumpkin purée – Provides moisture, natural sweetness, and that unmistakable pumpkin flavor. Use 100% pure pumpkin, not pumpkin pie filling.

Granulated sugar – Sweetens the muffins while helping create a light texture.

Brown sugar – Adds richness and a subtle molasses flavor to the batter.

Eggs – Bind the ingredients and add structure to both the muffins and the cheesecake filling.

Vegetable oil – Keeps the muffins moist without overpowering the pumpkin spice flavor.

Vanilla extract – Enhances the flavor of both the muffin batter and the cheesecake swirl.

Pumpkin pie spice – A warm blend of cinnamon, nutmeg, ginger, and cloves that defines the flavor of the muffins.

Baking soda – Helps the muffins rise and stay fluffy.

Salt – Balances the sweetness and enhances the spice.

Cream cheese – Softened cream cheese forms the creamy, tangy filling.

Powdered sugar – Sweetens the cream cheese filling without grittiness.

Directions

1. Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners.
2. In a large bowl, whisk together flour, pumpkin pie spice, baking soda, and salt. Set aside.
3. In another bowl, whisk together pumpkin purée, granulated sugar, brown sugar, eggs, oil, and vanilla extract until smooth.
4. Gradually fold the dry ingredients into the wet mixture until just combined—do not overmix.
5. In a small bowl, beat softened cream cheese with powdered sugar, an egg yolk, and vanilla until smooth.
6. Spoon muffin batter into liners, filling each about two-thirds full. Add a spoonful of the cream cheese mixture on top of each, then swirl gently with a toothpick or knife.
7. Bake for 18–22 minutes, or until a toothpick inserted into the muffin (not the cheesecake swirl) comes out clean.
8. Allow muffins to cool in the pan for 5 minutes before transferring to a wire rack.

Servings and timing

This recipe makes about 12 muffins. Prep time is 15 minutes, baking takes 20 minutes, and cooling adds 10 minutes. Total time is around 45 minutes.

Storage/reheating

Store Pumpkin Cheesecake Muffins in an airtight container in the refrigerator for up to 5 days. For longer storage, freeze them for up to 2 months and thaw overnight in the refrigerator. To enjoy warm, microwave for 10–15 seconds before serving.

Variations and Customizations

Pumpkin Cheesecake Muffins are versatile and can be adapted to suit your tastes.

For extra indulgence, sprinkle the muffins with streusel topping made of butter, flour, brown sugar, and cinnamon before baking. You could also add chocolate chips, pecans, or walnuts to the batter for added texture and flavor.

If you enjoy tangier cheesecake, mix a little sour cream into the cream cheese filling. For a less sweet version, reduce the powdered sugar in the cheesecake swirl. You can also experiment with spices—add a pinch of cardamom or allspice for a unique twist.

To make them dairy-free, substitute vegan cream cheese and use almond milk in the batter. A gluten-free flour blend also works well for those avoiding gluten. These small changes allow you to adapt the recipe without losing its cozy, seasonal charm.

FAQs

Can I use pumpkin pie filling instead of pumpkin purée?

No, pumpkin pie filling contains added sugar and spices that would alter the recipe.

Do I need to refrigerate these muffins?

Yes, because of the cheesecake filling, they should be stored in the refrigerator.

Can I freeze Pumpkin Cheesecake Muffins?

Yes, wrap them tightly and freeze for up to 2 months.

Can I make mini muffins with this recipe?

Yes, bake mini muffins for 10–12 minutes, checking for doneness early.

How do I make the swirl look nice?

Use a toothpick to gently swirl the cream cheese into the batter in circular motions.

Can I add a streusel topping?

Yes, it adds crunch and extra sweetness—just sprinkle it on before baking.

Conclusion

Pumpkin Cheesecake Muffins are the perfect blend of cozy pumpkin spice and creamy cheesecake, making them a standout treat for fall. They’re easy to prepare, beautifully swirled, and endlessly customizable, whether you prefer them simple, nutty, or topped with streusel. Ideal for breakfast, dessert, or festive gatherings, these muffins bring seasonal comfort in every bite.

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