Welcome to the ultimate autumn indulgence: these exquisite Pumpkin Cheesecake Muffins! Imagine the warm, comforting embrace of fall flavors harmoniously blended with a luscious, sweet cream cheese swirl. These muffins aren’t just a treat; they’re an experience. Impossibly moist, utterly irresistible, and surprisingly simple to prepare with just a handful of ingredients, they effortlessly transition from a delightful breakfast to a decadent dessert. Perfect for satisfying those seasonal cravings or impressing guests at your next gathering, they encapsulate everything wonderful about fall baking.
If you’re looking for other ways to enjoy the season’s bounty, explore our collection of beloved pumpkin recipes. For those who prefer a classic muffin without the cheesecake element, our Easy Pumpkin Muffins with brown sugar streusel offer a delightful alternative. And for a broader range of pumpkin-inspired delights, don’t miss our creamy Pumpkin Fluff Dip, the classic Pumpkin Cake with Cream Cheese Frosting, a hearty Pumpkin French Toast Bake, and the comforting Pumpkin Rice Pudding. Each recipe is crafted to bring the rich, spiced flavors of pumpkin into your home.

Why You’ll Fall in Love with These Pumpkin Cheesecake Muffins
These aren’t just any muffins; they are a celebration of autumn wrapped in a perfectly baked package. Here’s why they are destined to become your new favorite fall tradition:
- Bakery-Worthy Perfection: Forget dry, crumbly muffins! Ours boast an ultra-moist crumb that melts in your mouth, complemented by a beautiful, rich cream cheese swirl in every single bite. The visual appeal alone makes them look like they came straight from a gourmet bakery, yet they are incredibly easy to achieve in your own kitchen. You’ll be proud to serve these elegant treats.
- Cozy Autumn Flavors Elevated: Each muffin is a symphony of classic fall tastes. They are generously packed with the earthy sweetness of pumpkin, perfectly balanced by a warm blend of cinnamon and other comforting baking spices. The subtle tang and creamy texture of the cheesecake swirl cut through the spiced pumpkin, adding an extra layer of decadence that is simply irresistible. This flavor profile is pure autumn bliss.
- Perfect for Any Occasion: Their incredible versatility makes them suitable for a wide array of settings. Start your day with a comforting breakfast treat, enjoy them as a satisfying afternoon snack, or present them as a sophisticated dessert at holiday gatherings. Whether it’s a quiet morning coffee or a festive family brunch, these muffins are sure to be a crowd-pleaser, enchanting everyone with their sweet, spiced flavor and luxurious creamy swirl. They embody comfort and joy, making every moment a little more special.
The Ultimate Pumpkin Cheesecake Muffins: Simple & Delicious
As soon as the leaves start to change and the crisp air of fall arrives, these pumpkin and cream cheese swirl muffins become one of my most anticipated baking projects. There’s something truly magical about the aroma filling the kitchen, and the taste is absolutely divine. Beyond their deliciousness, they stand out for their incredible ease of preparation. You might be surprised to learn that the foundational muffin batter requires just four key ingredients, making this a quick and fuss-free recipe for even novice bakers.
The secret to our unbelievably easy pumpkin muffin base lies in a simple combination: a box of high-quality spice cake mix, a couple of fresh eggs, a touch of melted butter, and an entire can of pure pumpkin puree. This ingenious shortcut ensures a consistently moist, flavorful muffin every time, infused with all the comforting spices you love without needing to measure each one individually. These incredibly tender cake mix pumpkin muffins are then elevated with a rich and tangy cheesecake filling, delicately swirled into the batter before being baked to golden perfection.
The resulting muffins are a treat for the senses, perfect for any time of day. Imagine savoring one with a steaming cup of coffee to kickstart your morning, enjoying it as a delightful afternoon pick-me-up alongside a glass of warm apple cider, or transforming it into an unforgettable dessert by pairing it with a scoop of creamy vanilla ice cream. Their rich flavor and moist texture make them a versatile and cherished part of any fall menu, bringing comfort and joy with every bite.

Key Ingredients for Perfect Pumpkin Cheesecake Muffins
Crafting these delectable muffins requires a careful selection of ingredients, each playing a crucial role in achieving that perfect balance of flavor and texture. Here’s a detailed look at what you’ll need and some tips for the best results:
- Pumpkin Puree: The heart of our pumpkin muffins. For convenience and consistent results, the easiest route is to opt for unsweetened canned pumpkin puree. Ensure you grab pure pumpkin puree, not pumpkin pie filling, which contains added sugars and spices that will alter the recipe. For an extra touch of homemade goodness and if you have the time, you can also make your own Homemade Pumpkin Puree using small pie pumpkins or sugar pumpkins. This can impart an even fresher, deeper pumpkin flavor.
- Eggs: Essential for structure and moisture, eggs bind the ingredients together, contributing to the muffin’s tender crumb. Any type of large eggs will work perfectly. Always aim for fresh eggs for the best baking performance.
- Butter: We recommend using unsalted butter for this recipe. Using unsalted butter allows you to control the overall saltiness of the muffins, ensuring a balanced flavor profile. The butter should be melted and then allowed to cool slightly before incorporating it into the batter, preventing it from cooking the eggs. As a substitution, you can use an equal amount of vegetable oil for a slightly different texture, or for a lighter option, substitute half of the butter with unsweetened applesauce.
- Cake Mix: This is our secret weapon for simplicity and consistent flavor! Try to find a Spice Cake Mix, as it already contains a fantastic blend of pumpkin pie spices like cinnamon, nutmeg, ginger, and cloves, saving you from measuring individual spices. Popular brands like Betty Crocker and Duncan Hines often offer excellent versions of spice cake mix. If you can’t find spice cake mix, a yellow cake mix with an added teaspoon of pumpkin pie spice blend can work as a suitable alternative.
- Cream Cheese: The star of our irresistible cheesecake swirl! It is absolutely vital that your cream cheese is soft and at room temperature before you begin. This ensures that it blends smoothly with the other ingredients, creating a silky-smooth, lump-free filling. To achieve room temperature, simply pull it from the fridge at least 1 hour in advance. If you’re short on time, you can carefully transfer it to a microwave-safe container and heat it for about 20-30 seconds at a time until it reaches a softened, pliable consistency.
- Sugar: White granulated sugar is used in the cheesecake filling to provide sweetness and balance the tang of the cream cheese. It helps create that perfect, subtly sweet swirl that complements the spiced pumpkin muffin.
- Egg Yolk: A single large egg yolk is added to the cheesecake filling for richness and to help stabilize the mixture, giving it a beautifully creamy texture. You can either reserve the egg white for another culinary use, such as an omelet or meringue, or discard it if you prefer.
- Vanilla Extract: A touch of pure vanilla extract enhances the overall sweetness and complexity of the cheesecake swirl, adding a fragrant note that beautifully complements the other flavors. Use a good quality extract for the best aroma and taste.

How to Make Irresistible Pumpkin Cream Cheese Swirl Muffins
Creating these delightful fall muffins is a straightforward process that yields incredibly impressive results. Follow these simple steps for bakery-quality pumpkin cheesecake muffins right in your own kitchen:
- Prepare Your Workspace and Preheat Oven: Begin by preheating your oven to 350°F (175°C). This ensures your oven is at the correct temperature when the muffins are ready to bake, leading to an even rise. Next, prepare your muffin pans. Generously grease 24 standard muffin tins or line them with paper liners. Proper preparation prevents sticking and makes for easy removal.
- Whip Up the Pumpkin Muffin Batter: In a large mixing bowl, combine the can of pumpkin puree, two large eggs, and the melted and slightly cooled butter. Whisk these wet ingredients together thoroughly until the mixture is smooth and well-combined. This ensures all components are evenly distributed. Once smooth, add in the entire box of spice cake mix. Mix gently until just combined. Be careful not to overmix the batter; overmixing can lead to tough muffins. A few lumps are perfectly fine and often result in a more tender texture.
- Fill the Muffin Tins: Using an ice cream scoop (a 2-ounce scoop works perfectly for standard muffins) or a large spoon, scoop the prepared pumpkin batter evenly into each of the 24 muffin tins. Fill them approximately three-quarters of the way full. This allows enough room for the muffins to rise beautifully without overflowing.
- Craft the Creamy Cheesecake Topping: In a separate small bowl, combine the room temperature cream cheese, white granulated sugar, the large egg yolk, and the vanilla extract. Stir these ingredients together until the mixture is completely smooth and creamy, with no lumps of cream cheese remaining. The room temperature cream cheese is key here for an effortlessly smooth texture.
- Create the Iconic Swirl: Now for the fun part! Spoon about 1 tablespoon of the cheesecake mixture onto the top of each muffin batter-filled cup. Don’t worry about it being perfect at this stage. Then, take a clean toothpick or a small knife and gently swirl the cheesecake topping into the pumpkin muffin mix. Use a circular motion, or zig-zag patterns, to create a beautiful, marbleized effect. Avoid over-swirling, as you want distinct layers of pumpkin and cheesecake.
- Bake to Golden Perfection: Place the filled muffin pans into your preheated 350°F (175°C) oven. Bake for approximately 20-22 minutes. Baking time may vary slightly depending on your oven, so keep an eye on them. The muffins are done when they are golden brown on top, and a toothpick inserted into the center of a muffin comes out clean or with only a few moist crumbs attached.
- Cool and Serve: Once baked, carefully remove the muffin tins from the oven. Allow the muffins to cool in the tins for about 5-10 minutes. This allows them to set slightly and makes them easier to remove without breaking. After this initial cooling, transfer the muffins to a wire rack to cool completely at room temperature. Cooling them fully helps the cheesecake swirl to set properly and enhances their flavor and texture. Once cooled, these delightful Pumpkin Cheesecake Muffins are ready to be enjoyed!

Frequently Asked Questions About Pumpkin Cheesecake Muffins
Absolutely! These pumpkin cheesecake swirl muffins freeze exceptionally well, making them perfect for meal prep or enjoying a taste of fall long after the season ends. To freeze, ensure the muffins are completely cooled to room temperature. Then, arrange them in a single layer on a baking sheet and flash freeze for about an hour until firm. Once firm, transfer them to airtight freezer bags or containers, ensuring as much air is removed as possible to prevent freezer burn. They can be stored in the freezer for up to 2 months. Thaw overnight in the refrigerator or on the countertop for a few hours before serving.
For optimal freshness and to maintain the creamy texture of the cheesecake swirl, these muffins should be stored properly in an airtight container in the refrigerator. When stored in the fridge, they will stay fresh and delicious for up to 5 days. We recommend bringing them to room temperature for about 15-30 minutes before serving to fully appreciate their flavors and soft texture, or gently warming them.
The baking time for your pumpkin cream cheese muffins can vary depending on several factors, including the size of your muffins and the calibration of your oven. For standard-sized muffins baked in regular muffin tins at a preheated temperature of 350°F (175°C), you can expect them to bake to perfection in approximately 20-22 minutes. Always perform the toothpick test to confirm doneness.
If you opt for a mini-sized muffin pan, the baking time will significantly decrease, typically requiring only about 10-12 minutes. For a larger format, such as baking this recipe in loaf pans to create a pumpkin cheesecake bread, the bake time will increase. You can anticipate it taking closer to 30-35 minutes. Always ensure a toothpick inserted into the center comes out clean to guarantee they are fully baked.
Yes, while spice cake mix simplifies the process, you can make these muffins from scratch. You would need a standard pumpkin muffin recipe that uses all-purpose flour, sugar, baking powder, baking soda, and pumpkin pie spice, along with pumpkin puree, eggs, and butter. Just ensure the wet-to-dry ingredient ratio is similar to maintain the desired consistency for swirling the cheesecake mixture.
For the most defined swirl, avoid overmixing the cheesecake into the muffin batter. Dollop the cream cheese mixture generously on top of the muffin batter. Use a toothpick or the tip of a small knife to gently create a few swirls, pulling the cream cheese through the pumpkin batter. Two or three gentle swirls are usually enough to create a beautiful marbling effect without completely incorporating the two mixtures.
Expert Tips for Baking the Best Pumpkin Cheesecake Muffins
Achieving perfectly moist and flavorful pumpkin cheesecake muffins is simple with a few expert tips. Follow these guidelines to ensure your muffins turn out beautifully every time:
- Use Pure Pumpkin Puree, Not Pie Mix: This is a crucial distinction for the best flavor and texture. Pumpkin puree is 100% cooked pumpkin, while pumpkin pie mix contains added sweeteners and spices. Using pure pumpkin ensures you have full control over the flavor profile and consistency of your muffins. Always double-check the label!
- Avoid Overmixing the Batter: For muffins that are tender, light, and airy, mix the batter until just combined. Overmixing develops the gluten in the flour (from the cake mix), leading to a tougher, chewier muffin. A few small lumps in the batter are perfectly acceptable and often contribute to a softer crumb. Stop mixing as soon as you no longer see streaks of dry ingredients.
- Ensure Room Temperature Cream Cheese: Softened cream cheese is non-negotiable for a smooth cheesecake swirl. If your cream cheese is cold and hard, it will create lumps in your topping that won’t blend smoothly, resulting in an uneven texture. Planning ahead by letting it sit on the counter for at least an hour before baking is ideal. If you’re in a rush, a quick zap in the microwave (10-15 seconds at a time) can help, but be careful not to melt it.
- Swirl Gently for a Pretty Finish: To create that signature, eye-catching cheesecake swirl, dollop the cream cheese mixture on top of the muffin batter and use a toothpick or a small knife to gently swirl it in. A few gentle strokes are all you need. Over-swirling can cause the cheesecake to completely disappear into the batter, losing that beautiful marbled effect. Aim for a delicate touch.
- Fill Muffin Cups Generously: For those impressive, bakery-style muffins with beautiful, domed tops, fill your muffin cups generously. Fill them almost to the top, about ¾ to full. This allows the batter to rise and create that appealing domed shape during baking. Ensure your muffin tins are well-greased or lined to prevent any overflowing batter from sticking.
- Cool Completely for Best Results: While it’s tempting to dive into warm muffins, allowing them to cool completely is essential, especially for these cheesecake swirl muffins. Let them cool in the pan for a few minutes to set slightly, then transfer them to a wire rack to cool fully. This step is critical for the cheesecake swirl to set properly, preventing it from collapsing and ensuring a firm, creamy texture. Rushing this step can lead to a messy swirl and a less enjoyable experience.

Exciting Recipe Variations for Your Pumpkin Cheesecake Muffins
These pumpkin cheesecake muffins are wonderfully versatile, offering a fantastic base for creativity in the kitchen. Here are some delightful variations to try:
- Pumpkin Swirl Cupcakes: Elevate these muffins to dessert status by treating them as cupcakes. Once cooled, pipe a generous swirl of your favorite cream cheese frosting on top. Add a sprinkle of cinnamon or a decorative pumpkin candy for an extra festive touch. These are perfect for parties and special occasions.
- Pumpkin Cheesecake Bread: Transform this muffin recipe into a loaf by baking it in two 8”x4” loaf pans. After pouring the pumpkin batter into the pans, swirl the cheesecake topping into each loaf just before baking. The baking time will significantly increase compared to muffins; typically, it will take closer to 30-35 minutes, or even up to 45 minutes for a denser loaf. Keep a close eye on it and check for doneness by inserting a toothpick into the center of the loaf – if it comes out clean, your bread is perfectly baked.
- Gluten-Free Pumpkin Muffins: For those with dietary restrictions, it’s simple to adapt this recipe. Simply use a high-quality gluten-free spice cake mix to make your muffins entirely gluten-free. Most gluten-free cake mixes are designed to behave similarly to traditional ones, so no other major adjustments should be needed. Always check the packaging for specific instructions and ingredient lists.
- Delicious Add-ins: Enhance the texture and flavor of your pumpkin muffins with various mix-ins. Consider folding in a half-cup of chopped pecans or walnuts for a delightful nutty crunch. Chocolate chips (dark, semi-sweet, or white chocolate) are always a popular choice. For a touch of fruitiness, dried cranberries or chopped dried apricots can add a lovely tang and chewiness. Add these mix-ins to the pumpkin muffin batter after combining the cake mix, just before scooping into the pans.
- Mini Muffins for Little Hands (and Parties!): Bake the batter in mini muffin pans for a charming, bite-sized treat. These are perfect for baby showers, dessert buffets, or as a fun snack for kids. The baking time will be much shorter, typically around 10-12 minutes, so watch them closely.
- Streusel Topping: For an added layer of texture and sweetness, prepare a crumbly oat or cinnamon streusel. Sprinkle this mixture generously over the cheesecake swirl and muffin batter before baking. The streusel will bake to a golden-brown crunch, providing a delightful contrast to the soft muffin and creamy cheesecake.
Storing and Reheating Your Pumpkin Cheesecake Muffins
To ensure your Pumpkin Cheesecake Swirl Muffins remain as fresh and delicious as the day they were baked, proper storage is key. Here’s how to store and reheat them:
- Refrigerator Storage: Due to the cream cheese swirl, these muffins should always be stored in the refrigerator. Place your leftover Pumpkin Muffins with Cheesecake Swirl in an airtight container to prevent them from drying out and absorbing other fridge odors. Stored correctly, they will stay fresh and moist for up to 5 days. We highly recommend allowing them to come to room temperature for about 15-30 minutes before eating to fully appreciate their soft texture and nuanced flavors. Alternatively, a quick warm-up can also be delightful.
- Freezer Storage: These muffins are excellent candidates for freezing, making them a perfect make-ahead treat. Once completely cooled, place them in an airtight freezer-safe container or heavy-duty freezer bags. They will keep beautifully in the freezer for up to 2 months. To thaw, simply transfer them to the refrigerator overnight or let them sit on the countertop for a few hours. For a warm treat, you can gently reheat thawed muffins in the microwave for 15-30 seconds or in a low oven (300°F/150°C) for about 5-10 minutes until warmed through.
More Pumpkin Baking Recipes You’ll Love
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Pumpkin Cream Cheese Danish
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Pumpkin Muffins

Pumpkin Cheesecake Muffins Recipe
Ingredients
Pumpkin Muffins
- 1 15-ounce can pumpkin puree
- 2 large eggs
- 1/2 cup butter, melted and cooled
- 1 15.25-ounce box spice cake mix
Cheesecake Swirl Topping
- 8 ounces cream cheese, room temperature
- 1/4 cup sugar
- 1 large egg yolk
- 1 teaspoon vanilla extract
Instructions
- Preheat oven to 350 degrees F.
- Grease or line 24 muffin tins with paper liners and set aside.
- In a large mixing bowl, combine the pumpkin puree, eggs, and melted butter. Whisk together until smooth, then add the spice cake mix and mix until combined.
- Using an ice cream scoop or a spoon, scoop the batter into the prepared muffin tins, filling them about 3/4 of the way full.
- In a small bowl, combine the room temperature cream cheese, egg yolk, sugar, and vanilla and stir until smooth.
- Add about 1 tablespoon of cheesecake topping onto each muffin, then use a toothpick to swirl the cheesecake topping into the muffin mix.
- Bake for 20-22 minutes, or until golden brown and a toothpick inserted into the center comes out clean.
- Remove from the oven and let cool for a few minutes before removing the muffins from the muffin tin and cooling completely at room temperature. Enjoy!
Notes
Nutrition
Disclaimer: Nutritional values were calculated using a third-party tool and are provided as an estimation only.
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More of the Best Pumpkin Recipes to Try This Season
If you’re still craving more of that wonderful pumpkin flavor, we’ve got you covered! Explore these other fantastic pumpkin recipes that are perfect for any occasion:
- Homemade Pumpkin Spice Syrup: Elevate your coffee and desserts with this fragrant, easy-to-make syrup.
- Classic Pumpkin Pie: A timeless holiday favorite that’s always a hit.
- Creamy Pumpkin Rice Pudding: A comforting dessert that’s perfect for a cozy evening.
- Decadent Stuffed French Toast with Pumpkin: A breakfast or brunch showstopper that’s surprisingly easy.
- No-Bake Pumpkin Cheesecake: All the flavor of cheesecake with none of the baking hassle.
- Healthy Einkorn Pumpkin Muffins: A wholesome twist on classic pumpkin muffins.
- Discover even more delightful Fall Recipes to celebrate the season.
- Explore our wide array of Breakfast Recipes for every morning.
- Find more delicious and easy Quick Bread Recipes that come together in a flash.
These Pumpkin Cream Cheese Swirl Muffins are a true embodiment of autumn, offering a perfect blend of rich, spiced pumpkin and a luscious, tangy cheesecake swirl. They are incredibly moist, irresistibly delicious, and wonderfully versatile, serving equally well as a comforting breakfast, a delightful snack, or a decadent dessert. We hope you enjoy baking and savoring these delightful treats as much as we do!
