As the leaves begin to turn and the air gets crisp, I often find myself reaching for the flavors of fall, and nothing brings that warmth into my kitchen quite like Pumpkin Cheesecake Muffins. These delightful treats showcase a moist, spiced pumpkin exterior, hiding a silky cheesecake center that is bound to impress. With their quick prep time and versatile nature, they are not only an easy way to satisfy your sweet tooth but also a joyful addition to any fall gathering. Whether you’re hosting a festive brunch or simply enjoying a cozy afternoon at home, these muffins are sure to elevate your baking game. Curious how to whip up these seasonal delights? Let’s dive into the recipe!

Why Are Pumpkin Cheesecake Muffins a Must-Try?
Irresistible combination of flavors: The fusion of pumpkin spice and creamy cheesecake creates an explosion of taste that will leave you craving more.
Quick prep time: Ready in just under 30 minutes, making them perfect for a spontaneous fall treat or a last-minute dessert for guests.
Versatile variations: Feel free to get creative! Add nuts or chocolate chips for extra texture, or swap out spices to adjust the flavor profile.
Ideal for sharing: Share them with friends and family at gatherings; their delightful taste is sure to earn rave reviews!
Nutrient-packed: Not only delicious, but these muffins also offer benefits from pumpkin and eggs, making them a comforting yet enjoyable option!
For more scrumptious ideas, check out our fall baking collection.
Pumpkin Cheesecake Muffin Ingredients
For the Muffins
- All-purpose Flour – Provides structure; can substitute with gluten-free flour for a different texture.
- Sugar – Adds sweetness; use brown sugar for extra moisture and a caramel-like flavor.
- Baking Powder – Leavening agent for rising; ensure it’s fresh for best results.
- Baking Soda – Helps the muffins rise while neutralizing pumpkin acidity.
- Cinnamon – Adds warmth and spice; experiment with nutmeg or pumpkin pie spice for variety.
- Nutmeg – Delivers depth of flavor; use in smaller amounts for a more subtle taste.
- Salt – Enhances sweetness; consider kosher salt for a coarser texture.
- Vegetable Oil – Adds moisture and richness; can be substituted with melted coconut oil for a tropical twist.
- Eggs – Binds ingredients and aids in rising; flaxseed eggs serve as a vegan alternative.
- Pumpkin Puree – The star ingredient for flavor; use well-drained fresh puree or canned.
- Vanilla Extract – Enhances flavor complexity and sweetness.
For the Cream Cheese Filling
- Cream Cheese – Provides the rich, creamy center; ensure it’s softened for easy mixing.
- Cream Cheese Filling Sugar – Sweetens the filling; reduce the amount for a less sweet option.
- Extra Egg for Filling – Binds the cheesecake mixture nicely.
- Vanilla Extract for Filling – Elevates the flavor of the cheesecake component.
These Pumpkin Cheesecake Muffin ingredients come together to create a delightful fall treat that combines moist pumpkin goodness with a creamy surprise!
Step‑by‑Step Instructions for Pumpkin Cheesecake Muffins
Step 1: Preheat the Oven
Begin by preheating your oven to 350°F (175°C). While the oven warms up, prepare your muffin tin by placing paper liners in each cup to prevent sticking and ensure easy cleanup later on.
Step 2: Prepare the Dry Mix
In a medium mixing bowl, whisk together 2 cups of all-purpose flour, 1 cup of sugar, 2 teaspoons of baking powder, 1 teaspoon of baking soda, 1 teaspoon of ground cinnamon, ½ teaspoon of nutmeg, and ½ teaspoon of salt. This blend creates a flavorful foundation for your Pumpkin Cheesecake Muffins, so make sure there are no lumps for a smooth batter.
Step 3: Combine Wet Ingredients
In a large bowl, whisk together ½ cup of vegetable oil, 2 large eggs, 1 cup of pumpkin puree, and 2 teaspoons of vanilla extract. Mix until the ingredients are well combined and smooth. The wet mixture should have a rich, creamy consistency, which will bring moisture and flavor to the muffins.
Step 4: Mix Together
Gently fold the dry ingredients into the wet mixture using a spatula. Stir just until combined; be careful not to overmix, as this can lead to tough muffins. The batter should remain slightly lumpy, ensuring that the Pumpkin Cheesecake Muffins stay moist and tender.
Step 5: Make Cheesecake Filling
In another bowl, beat together 8 ounces of softened cream cheese, ¼ cup of sugar, 1 extra egg, and 1 teaspoon of vanilla extract. Mix until creamy and smooth, creating a luscious filling that contrasts beautifully with the spiced pumpkin batter. Set this aside while you finish assembling the muffins.
Step 6: Assemble Muffins
Fill each muffin liner halfway with the pumpkin batter. Then, add a generous spoonful of the cheesecake filling in the center, and top with more pumpkin batter until each cup is about ¾ full. This layering technique ensures that each bite of your Pumpkin Cheesecake Muffins has that delightful surprise center.
Step 7: Bake
Place the muffin tin in the preheated oven and bake for 20-25 minutes. They’re done when a toothpick inserted into the pumpkin muffin part comes out clean, ensuring the muffins are fully cooked while still being moist. They should be golden brown on the edges.
Step 8: Cool
Once baked, remove the muffins from the oven and let them cool in the tin for about 5 minutes. Afterward, carefully transfer them to a wire rack to cool completely. This step prevents sogginess by allowing air to circulate around the muffins. Enjoy the aroma as these Pumpkin Cheesecake Muffins cool!

What to Serve with Pumpkin Cheesecake Muffins
Elevate your fall gatherings with delightful companions that highlight the flavors of these luscious muffins.
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Creamy Mashed Potatoes: The buttery smoothness is an ideal contrast to the spiced pumpkin, creating a comforting balance on your plate.
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Warm Apple Cider: A fragrant drink that enhances the fall experience, pairing perfectly with the sweet and spicy notes of the muffins.
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Roasted Brussels Sprouts: Their crispy outer layer brings a textural contrast and slight bitterness that complements the muffins’ sweetness beautifully.
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Maple Glazed Carrots: The sweet, caramelized flavors of maple enhance the pumpkin notes, making them a pleasing side dish for a harmonious meal.
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Spiced Pecans: These add crunchy texture and a maple hint, providing a savory bite to complement the softness of the muffins, creating a delightful munching experience.
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Vanilla Ice Cream: Serve it warm and drizzled with caramel sauce alongside the muffins for an indulgent dessert combo, turning your cozy afternoon into a treat-filled festivity.
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Pumpkin Spice Latte: Indulge in this divine pairing that amplifies the warm, cozy flavors shared by both the drink and the dessert.
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Cranberry Sauce: The tartness of cranberry provides a bright counterpoint, enhancing flavor depth while refreshing the palate with each bite.
How to Store and Freeze Pumpkin Cheesecake Muffins
Fridge: Store muffins in an airtight container for up to 1 week. This keeps them fresh while preserving their delightful texture and flavor.
Freezer: Freeze Pumpkin Cheesecake Muffins individually wrapped in plastic wrap, then placed in a zip-top bag. They will stay good for up to 3 months.
Thawing: To enjoy, simply remove a muffin from the freezer and thaw it overnight in the fridge or reheat it in the microwave for about 20-30 seconds until warm.
Reheating: If you prefer a warm treat, reheat on a microwave-safe plate for a few seconds or in a preheated oven at 350°F (175°C) for 5-7 minutes before serving to restore freshness.
Expert Tips for Pumpkin Cheesecake Muffins
- Avoid Overmixing: Gently fold the batter to maintain tenderness. Overmixing can yield tough muffins, which no one wants!
- Careful with Filling: Limit cheesecake filling to one spoonful per muffin to prevent overflow during baking.
- Use Well-Drained Pumpkin: Ensure your fresh pumpkin puree is well-drained; excess moisture can make muffins soggy.
- Fresh Ingredients Matter: Always check that your baking powder and baking soda are fresh for maximum rise and fluffiness.
- Make Ahead: These Pumpkin Cheesecake Muffins store well. You can make them in advance and freeze for later enjoyment!
Pumpkin Cheesecake Muffins: Endless Possibilities
Feel free to get creative with these delightful muffins and make them your own!
- Gluten-Free: Replace all-purpose flour with your favorite gluten-free flour blend for a delicious alternative.
- Sweet Potato Swap: Substitute half the pumpkin puree with sweet potato puree for a unique, earthy flavor.
- Chocolate Indulgence: Fold in chocolate chips to the batter for a rich and decadent surprise in every bite.
- Nutty Twist: Add chopped walnuts or pecans to the batter for delightful crunch and added nutrition.
- Spice Variations: Experiment with ginger or allspice for a different flavor profile that dances on the palate.
- Vegan Delight: Use flaxseed eggs and dairy-free cream cheese to make these muffins completely plant-based.
- Mini Muffins: Bake these in mini muffin tins for bite-sized treats that are perfect for snack time or gatherings.
- Maple Glaze: Drizzle a simple maple glaze over the cooled muffins for a sweet finish that enhances their fall flavor.
Dive into your own autumn adventure with these scrumptious twists! For more delicious ideas, check out our fall baking collection or discover more about pumpkin’s versatility in baking with our article on heartwarming fall desserts.
Make Ahead Options
These Pumpkin Cheesecake Muffins are perfect for meal prep enthusiasts! You can mix the dry ingredients and store them in an airtight container for up to 3 days before you bake. Additionally, the cheesecake filling can be prepared and refrigerated for up to 24 hours; simply cover it tightly to maintain its creamy consistency. When you’re ready to bake, combine the wet and dry ingredients with the cheesecake filling as instructed. This approach not only saves time but allows you to enjoy fresh, homemade muffins with minimal effort. Just follow the bake and cool instructions, and you’ll have delightful treats ready to wow your family!

Pumpkin Cheesecake Muffins Recipe FAQs
What type of pumpkin is best for muffins?
Absolutely! For the best flavor, I recommend using fresh pumpkin puree made from sugar pumpkins, also known as pie pumpkins. These smaller pumpkins have a sweeter, denser flesh compared to larger varieties typically used for decoration. You can also use canned pumpkin puree; just ensure it’s 100% pumpkin, not pie filling.
How should I store Pumpkin Cheesecake Muffins?
Very! Store your muffins in an airtight container at room temperature for 2-3 days for optimal freshness. If you want them to last longer, refrigerate them for up to a week; just ensure they’re in an airtight container to prevent them from drying out.
Can I freeze Pumpkin Cheesecake Muffins?
Definitely! To freeze, wrap each muffin individually in plastic wrap and place them in a zip-top freezer bag. They can be frozen for up to 3 months. When you’re ready to enjoy, thaw them overnight in the fridge or pop them in the microwave for about 20-30 seconds to warm them up.
What should I do if my muffins are too dense?
Ah, don’t worry! If your muffins turn out dense, it’s often due to overmixing the batter or using old leavening agents. Ensure you gently fold the wet and dry ingredients together until just combined. Additionally, check that your baking powder and soda are fresh; they can lose potency over time!
Are these muffins suitable for people with dietary restrictions?
Yes! To make these muffins vegan, substitute the eggs with flaxseed eggs (1 tablespoon of ground flaxseed mixed with 2.5 tablespoons of water per egg, let sit for 5 minutes) and use dairy-free cream cheese. For those with gluten sensitivities, replacing all-purpose flour with a gluten-free flour blend works wonderfully too.
How can I tell if my muffins are fully baked?
Great question! To check for doneness, insert a toothpick into the muffin’s pumpkin portion. If it comes out clean, the muffins are ready. Remember, if it picks up any cheesecake filling, that’s not a reliable test! Let them cool slightly before handling for the best texture.

Pumpkin Cheesecake Muffins: Your Fall Flavor Adventure
Ingredients
Equipment
Method
- Preheat your oven to 350°F (175°C) and prepare your muffin tin with paper liners.
- In a medium bowl, whisk together the flour, sugar, baking powder, baking soda, cinnamon, nutmeg, and salt.
- In a large bowl, mix the vegetable oil, eggs, pumpkin puree, and vanilla extract until smooth.
- Fold the dry mixture into the wet ingredients until just combined, being careful not to overmix.
- For the filling, beat together cream cheese, sugar, extra egg, and vanilla until creamy and smooth.
- Fill muffin liners halfway with pumpkin batter, add cheesecake filling, then top with more pumpkin batter.
- Bake for 20-25 minutes or until a toothpick comes out clean. They should be golden brown.
- Cool in the tin for 5 minutes before transferring to a wire rack to cool completely.

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