As the leaves turn golden and the air fills with the earthy scent of autumn, there’s nothing quite like the smell of freshly baked goods wafting through the kitchen. Today, I’m thrilled to share my beloved recipe for Pumpkin Cheesecake Muffins that perfectly capture the spirit of the season. These delightful delights combine moist pumpkin spice muffin batter with a creamy cheesecake swirl, creating a unique treat that is both indulgent and light. Not only are they easy to whip up, making them perfect for your busy mornings or last-minute gatherings, but they also double as a cozy dessert option that’s sure to impress your family and friends. So, what will you pair with these luscious muffins—an afternoon tea or an evening coffee?

Why Are These Muffins So Irresistible?
Unique Flavor Fusion: Combining spiced pumpkin and rich cheesecake creates an indulgent treat that captures the essence of fall.
Easy Prep: With simple ingredients, these muffins come together effortlessly, perfect for both novice and seasoned bakers.
Versatile Treat: Enjoy them for breakfast, snack time, or dessert—these muffins are flexible enough for any occasion.
Crowd-Pleasing: Their delightful taste will impress your family and friends, making them a hit at gatherings.
Time-Saving: You can whip up these Pumpkin Cheesecake Muffins in under 30 minutes, making them ideal for busy schedules! Pair them with a warm drink, and you’ll have a perfect autumn experience.
Pumpkin Cheesecake Muffin Ingredients
For the Muffin Batter
- All-purpose flour – Provides the structure; can easily be swapped with a gluten-free blend for a lighter option.
- Baking powder – Acts as a leavening agent, ensuring your muffins rise beautifully.
- Baking soda – Works alongside the pumpkin puree to create that perfect fluffy texture.
- Cinnamon – Offers warm, comforting spice; feel free to adjust to match your flavor preference.
- Nutmeg – Enhances the fall flavor; a little goes a long way!
- Cloves – Adds depth and warmth; you can omit if you’re not a fan of strong spices.
- Salt – Balances sweetness and enhances overall flavors.
- Granulated sugar – Sweetens the base of the muffins; brown sugar adds moisture and richness.
- Brown sugar – Complements the pumpkin flavor with a hint of caramel.
- Pumpkin puree – The star ingredient that brings that lovely autumn flavor; make sure it’s pure, not spiced.
- Eggs – Bind the ingredients together while adding moisture and richness.
- Oil – Keeps the muffins moist; substitute with melted butter or applesauce for a lighter touch.
- Vanilla extract – Enhances the overall flavor profile of these Pumpkin Cheesecake Muffins.
For the Cheesecake Swirl
- Cream cheese – Essential for that creamy cheesecake layer; full-fat is preferred for the best texture.
- Egg yolk – Adds richness and smoothness to the cheesecake swirl.
- Granulated sugar – Sweetens the cheesecake component, making it a perfect complement to the spiced muffin batter.
- Vanilla extract – A splash adds a lovely depth to the cheesecake layer.
Happy baking, and enjoy every moment of creating these delicious Pumpkin Cheesecake Muffins!
Step‑by‑Step Instructions for Pumpkin Cheesecake Muffins
Step 1: Preheat and Prepare
Preheat your oven to 350°F (175°C) to create the perfect baking environment for your Pumpkin Cheesecake Muffins. While the oven heats, line a 12-cup muffin tin with liners or spray the cups with non-stick spray to ensure easy removal of those delicious treats once baked.
Step 2: Whisk Dry Ingredients
In a large bowl, whisk together the all-purpose flour, baking powder, baking soda, cinnamon, nutmeg, cloves, and salt. This step ensures that the dry ingredients are properly mixed, allowing for even rising and flavor distribution in your muffin batter. Set aside your dry mixture, as we’ll combine it with the wet ingredients shortly.
Step 3: Mix Wet Ingredients
In another bowl, combine granulated sugar, brown sugar, pumpkin puree, eggs, oil, and vanilla extract. Using a whisk, mix everything until smooth and creamy, creating a delightful base for your Pumpkin Cheesecake Muffins. This blend of ingredients will provide moisture and flavor, so ensure there are no clumps.
Step 4: Combine Wet and Dry Ingredients
Fold the wet ingredients into the dry mixture using a rubber spatula. Gently combine until just incorporated; avoid overmixing as it could lead to dense muffins. The goal is to have a semi-thick batter with little to no dry flour visible—this will ensure your muffins rise beautifully in the oven.
Step 5: Prepare Cheesecake Mixture
In a small bowl, beat the cream cheese, granulated sugar, egg yolk, and vanilla extract together until creamy and smooth. This rich, velvety cheesecake mixture will add a decadent swirl to your Pumpkin Cheesecake Muffins, creating a delightful contrast with the spiced pumpkin flavor.
Step 6: Fill Muffin Cups
Spoon about 2 tablespoons of the pumpkin batter into each muffin cup, filling them just under halfway. Next, add 1 tablespoon of the cream cheese mixture on top of the pumpkin batter. Use a toothpick to lightly swirl the cheesecake into the muffin batter, creating beautiful marbling for each muffin.
Step 7: Bake to Perfection
Place the muffin tin in the preheated oven and bake for 22-25 minutes. Start checking for doneness around 20 minutes by inserting a toothpick into the center of a muffin. When it comes out clean or with a few moist crumbs, your Pumpkin Cheesecake Muffins are ready to be removed from the oven. Let them cool slightly before serving.

Expert Tips for Perfect Pumpkin Cheesecake Muffins
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Avoid Overmixing: Gently fold the wet and dry ingredients together; overmixing can lead to dense muffins instead of fluffy ones.
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Check for Doneness Early: Begin checking your muffins for doneness around the 20-minute mark to prevent overbaking and keep them moist.
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Use Room Temperature Ingredients: Incorporating ingredients like eggs and cream cheese at room temperature creates a smoother batter, ensuring even baking.
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Swirl with Care: When creating the cheesecake swirl, use a toothpick to gently pull through the batter—don’t mix it in completely to maintain that glorious marbled effect.
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Keep Muffins Fresh: Store your Pumpkin Cheesecake Muffins in an airtight container in the refrigerator for up to 5 days to maintain their moist texture.
How to Store and Freeze Pumpkin Cheesecake Muffins
Fridge: Store your Pumpkin Cheesecake Muffins in an airtight container for up to 5 days. This will help retain their moist texture and delightful flavors.
Freezer: For longer storage, freeze muffins in a single layer on a baking sheet, then transfer them to a zip-top freezer bag. They can be frozen for up to 3 months.
Reheating: To enjoy fresh-baked taste, reheat muffins in the microwave for 15-20 seconds or in a preheated oven at 350°F (175°C) for about 5-7 minutes, until warm.
Make-Ahead: You can prepare the batter a day in advance and store it in the fridge. Bake your Pumpkin Cheesecake Muffins just before serving for a warm, cozy treat!
What to Serve with Pumpkin Cheesecake Muffins
As you savor the creamy goodness of these muffins, think about what complements their warm, spiced flavors beautifully.
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Warm Spiced Chai: This aromatic blend of tea and spices perfectly echoes the muffin’s warm notes, enhancing your cozy experience. Enjoying a cup while letting the flavors mingle truly elevates the occasion.
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Creamy Hot Cocoa: Rich hot cocoa adds a sweet, chocolaty contrast to the muffins. The warmth of the beverage makes for an indulgent treat on chilly autumn days, bringing a sense of comfort and nostalgia.
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Maple Pecan Granola: Crunchy granola with hints of maple and pecans offers a delightful texture contrast. Sprinkle it on top of the muffins for added crunch or enjoy it as a side for a satisfying morning meal.
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Apple Cider: This classic fall beverage complements the pumpkin’s sweetness beautifully while adding a refreshing, crisp note. Sip on warm apple cider alongside your muffins for a seasonal celebration.
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Vanilla Ice Cream: For a decadent dessert twist, serve these muffins warm with a scoop of creamy vanilla ice cream. The contrast of temperatures and textures creates an unforgettable treat that everyone will love.
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Cinnamon Sugar Donuts: Pair these muffins with fluffy cinnamon sugar donuts for a delightful brunch spread. Their overlapping flavors will leave your guests craving more!
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Spiced Coffee: Brew a pot of coffee with a hint of cinnamon or nutmeg for a warm embrace that ties the meal together. This adds a comforting touch that turns breakfast or brunch into something magical.
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Pumpkin Spice Latte: Embrace the season with a luscious pumpkin spice latte which mirrors the flavor of the muffins. This sweet, spiced drink is the perfect complement to your cozy morning ritual.
Pumpkin Cheesecake Muffins Variations & Substitutions
Feel free to make these Pumpkin Cheesecake Muffins your own by trying out these delightful variations!
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Gluten-Free: Use a 1:1 gluten-free flour blend instead of all-purpose flour for a celiac-friendly option without compromising flavor.
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Dairy-Free: Substitute the cream cheese with a vegan cream cheese alternative for a delicious plant-based version; this keeps the muffins creamy and decadent.
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Less Sugar: Replace granulated sugar with coconut sugar or maple syrup for a healthier sweetener that enhances the muffins’ richness.
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Pumpkin Spice Boost: Add 2 teaspoons of pumpkin pie spice blend to your dry mixture for an even more robust autumn flavor.
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Nutty Addition: Toss in some chopped walnuts or pecans into the muffin batter for a satisfying crunch that complements the soft texture.
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Boozy Twist: Add 1 tablespoon of bourbon or rum to the wet mixture for a subtle kick that lifts the festive flavors.
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Chocolate Lovers: Fold mini chocolate chips into the muffin batter for a sweet surprise that plays beautifully with the pumpkin and cheesecake layers.
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Fruity Infusion: Mix in some fresh cranberries or applesauce for a tangy twist that adds moisture and vibrant flavor to these muffins.
For serving suggestions, enjoy them alongside a steaming cup of chai spice tea or add a dollop of your favorite cream cheese frosting for an indulgent treat at your next fall gathering!
Make Ahead Options
These Pumpkin Cheesecake Muffins are a fantastic choice for meal prep! You can prepare the muffin batter and cheesecake swirl separately up to 24 hours in advance. Store the pumpkin batter in an airtight container in the refrigerator, while the cheesecake mixture should be kept in a separate container. When you’re ready to bake, simply pull both out, spoon the pumpkin batter into the muffin tins, add the cheesecake mixture, and swirl as directed. This method not only saves you time on busy mornings but ensures that your muffins are just as delicious and airy when baked! Enjoy the delightful aroma filling your kitchen with minimal effort!

Pumpkin Cheesecake Muffins Recipe FAQs
What kind of pumpkin puree should I use?
Absolutely! Ensure you’re using pure pumpkin puree, not a spiced variety. Look for cans that specify “100% pumpkin” on the label; this ensures a rich and balanced flavor that’s essential for your muffins.
How should I store leftover muffins?
To keep your Pumpkin Cheesecake Muffins fresh, place them in an airtight container in the refrigerator for up to 5 days. This will maintain their lovely moisture and flavor. Alternatively, you can enjoy them warm by reheating them briefly in the microwave!
Can I freeze Pumpkin Cheesecake Muffins?
Very! To freeze your muffins, place them in a single layer on a baking sheet to prevent sticking, then freeze until solid. Once frozen, transfer them to a zip-top freezer bag. They’re good for up to 3 months! To thaw, just leave them at room temperature or warm them in the microwave for a cozy treat.
What do I do if the muffins turn out dense?
If your muffins are dense, it’s likely due to overmixing. When combining wet and dry ingredients, mix just until no dry flour is visible. Also, make sure your baking powder and baking soda are fresh—if they’ve been sitting for a while, they may not work as effectively!
Are these muffins suitable for my pet?
While Pumpkin Cheesecake Muffins are delightful for humans, they contain sugar and cream cheese, which are not ideal for pets. I recommend keeping these treats for yourself and opting for plain pumpkin puree (without spices or sweeteners) if you want to share a little with your furry friend.
Can I substitute any ingredients for dietary restrictions?
Absolutely! You can swap all-purpose flour with a gluten-free flour blend for a gluten-free version. For a lighter option, use applesauce in place of oil. If you’re managing sugar intake, consider reducing the granulated sugar or using a sugar alternative while still letting that pumpkin shine through!

Pumpkin Cheesecake Muffins That'll Warm Your Heart This Fall
Ingredients
Equipment
Method
- Preheat your oven to 350°F (175°C) and prepare a muffin tin with liners or non-stick spray.
- In a large bowl, whisk together the flour, baking powder, baking soda, cinnamon, nutmeg, cloves, and salt.
- In another bowl, mix granulated sugar, brown sugar, pumpkin puree, eggs, oil, and vanilla until smooth.
- Fold the wet ingredients into the dry mixture until just combined; do not overmix.
- In a small bowl, beat the cream cheese, granulated sugar, egg yolk, and vanilla until creamy.
- Spoon 2 tablespoons of pumpkin batter into each muffin cup, followed by 1 tablespoon of cheesecake mixture. Swirl gently with a toothpick.
- Bake for 22-25 minutes, checking for doneness around 20 minutes.

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