Irresistible Pumpkin Cheesecake Cupcakes with Brown Sugar Marshmallow Frosting
Indulge in the ultimate fall treat with these incredible pumpkin cheesecake cupcakes! Each bite delivers a harmonious blend of moist, spiced pumpkin cupcake, a creamy, tangy cheesecake center baked right in, and a crown of fluffy, light brown sugar marshmallow frosting. This isn’t just a cupcake; it’s a complete dessert experience that captures the essence of autumn.
As the leaves begin to turn and the air grows crisp, there’s a universal craving for all things pumpkin. While classic pumpkin treats are always welcome, sometimes you want something truly extraordinary. That’s where these Pumpkin Cheesecake Cupcakes step in, offering a delightful twist on your favorite fall flavors. If you adore pumpkin cupcakes, you might also want to explore our classic Pumpkin Cupcakes with Cream Cheese Frosting for another timeless option, but prepare for an elevated experience with today’s recipe.

I originally shared this recipe way back on November 18, 2009. In those early days, my blog posts were often quite concise – mostly just the recipe without much fanfare or a deep dive into the baking process. Over the years, my passion for baking and sharing recipes has grown, and with it, my understanding of how to truly perfect a dish and present it in the most helpful way possible. So, I decided it was high time to revisit this beloved recipe, give it a fresh look, and share all the refined details with you, essentially hitting the “restart” button on a true autumnal gem.
We’re already several days into October, and I confess, I’ve been a little behind on my pumpkin recipe game this season. And frankly, I hadn’t planned on posting another sweet recipe today, especially with a whole week of delightful treats already lined up. But I simply couldn’t resist bringing these beauties back into the spotlight. As I browsed through the archives of Taste and Tell, the memory of these pumpkin cheesecake cupcakes surfaced, and I knew instantly that I had to make them again – and share their perfected version with all of you.
What could possibly be better than a perfectly spiced pumpkin cupcake? How about one that’s generously stuffed with a creamy, rich cheesecake mixture, creating an incredible surprise in every bite? And just when you think it couldn’t get any better, imagine it topped with a dreamy, light-as-air brown sugar marshmallow frosting! This combination is truly what dessert dreams are made of, blending the comforting warmth of pumpkin with the luxurious tang of cheesecake and the whimsical sweetness of marshmallow.

My culinary journey has definitely evolved over the past few years, and with it, my skills in the kitchen have, I believe, significantly improved. This growth allowed me to approach this classic recipe with a fresh perspective, leading to a few crucial tweaks that have made it absolutely perfect. The original recipe stated it yielded 12 cupcakes, but as I was filling the muffin cups, I kept having a nagging feeling that they were just too full. I should have trusted my instincts! While they didn’t completely overflow, the resulting cupcakes were far from the ideal shape and texture I envisioned.
After a round of dedicated testing and trying again, I conclusively decided that 18 cupcakes was the magic number. This adjustment ensures that each cup is filled to the perfect amount, leading to beautifully baked, evenly risen, and perfectly proportioned pumpkin cheesecake cupcakes every single time. The slight increase in yield means more deliciousness to share (or to secretly enjoy yourself!).
Honestly, you could stop right there after the cupcakes cool, and you’d have an incredibly delicious treat on your hands. Some might even call them muffins without frosting, and they’d be right – a delightful breakfast or snack option! But the true magic, the undeniable “wow” factor, comes from the brown sugar marshmallow frosting. Before I tried it, I would have never imagined that the perfect companion for the rich, spiced pumpkin and creamy cheesecake would be a marshmallow frosting. Yet, the moment these flavors come together, it’s clear they are an absolutely perfect match, creating an unforgettable dessert symphony.
These Pumpkin Cheesecake Cupcakes embody just one of the many reasons why I absolutely adore fall baking. It’s the season for cozy flavors, warm spices, and creating comforting treats that bring joy to family and friends. The aroma filling your kitchen as these bake is simply intoxicating, a true herald of autumn’s bounty.

Essential Baking Tips for Flawless Cupcakes
Achieving bakery-quality cupcakes at home is entirely possible with a few key techniques. Here are my top tips for ensuring your Pumpkin Cheesecake Cupcakes turn out perfectly:
- Room Temperature Ingredients: Always ensure your cream cheese, eggs, and pumpkin puree are at room temperature. This helps them incorporate smoothly, creating a uniform batter and preventing lumps in your cheesecake filling.
- Do Not Overmix: When combining the wet and dry ingredients for the pumpkin cupcake batter, mix only until just combined. Overmixing can develop the gluten in the flour, leading to dense, tough cupcakes. A light hand will ensure a tender, moist crumb.
- Careful Cupcake Filling: Pay close attention to the layering process. A tablespoon of pumpkin batter, followed by a dollop of cheesecake, and then another spoonful of pumpkin batter ensures the cheesecake remains perfectly centered and doesn’t sink or overflow. Filling each cup about 2/3 full is crucial for optimal rise and to prevent spilling.
- Don’t Overbake: Keep a close eye on your cupcakes. Overbaking will dry them out. They are done when a toothpick inserted into the pumpkin portion (avoiding the cheesecake center) comes out clean, and the tops spring back lightly when touched.
- Cool Completely: Resist the urge to frost warm cupcakes! The marshmallow frosting, in particular, requires a completely cooled surface to adhere properly and maintain its fluffy texture. Patience is key for a beautifully finished product.
Creative Variations to Explore
While this recipe is perfect as is, you can always put your own spin on it! Here are a few ideas to customize your pumpkin cheesecake cupcakes:
- Spice it Up: Feel free to adjust the pumpkin pie spice blend. You could add a pinch of ground ginger, extra cinnamon, or a hint of cloves for a more intense spice profile.
- Topping Temptations: Before adding the frosting, sprinkle a little cinnamon sugar, crushed pecans, or even a drizzle of caramel sauce on top of the cooled cupcakes for an extra layer of flavor and texture.
- Alternative Frosting (If You Must!): While the brown sugar marshmallow frosting is highly recommended, if you’re short on time or prefer a different flavor, a classic cream cheese frosting would also be delicious, or a simple vanilla buttercream.
- Miniature Marvels: Adapt the recipe for mini cupcakes by adjusting baking time. These bite-sized treats are perfect for parties or when you just need a small indulgence.
Storing Your Delicious Creations
To keep your Pumpkin Cheesecake Cupcakes fresh and delicious, proper storage is essential:
- Room Temperature: Unfrosted cupcakes can be stored in an airtight container at room temperature for up to 2 days.
- Refrigeration: Once frosted, these cupcakes are best stored in an airtight container in the refrigerator due to the cream cheese filling and egg white frosting. They will last for up to 3-4 days. Allow them to come to room temperature for about 15-20 minutes before serving for the best flavor and texture.
- Freezing: Both unfrosted and frosted cupcakes can be frozen. For unfrosted cupcakes, wrap them individually in plastic wrap, then place them in an airtight freezer bag for up to 2-3 months. Thaw at room temperature before frosting. For frosted cupcakes, flash freeze them on a baking sheet until the frosting is firm, then wrap individually and store in a freezer bag. Thaw in the refrigerator before bringing to room temperature.
More Pumpkin Recipes
Can’t get enough of pumpkin? Here are some other fantastic fall recipes to try:
Pumpkin Cinnamon Rolls
Pumpkin Fudge
Oatmeal Pumpkin Chocolate Chip Cookies
Pumpkin Waffles
Pumpkin Snickerdoodles
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Pumpkin Cheesecake Cupcakes with Brown Sugar Marshmallow Frosting
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Ingredients
Cheesecake Filling:
- 1 (8 oz) package cream cheese softened
- 1/2 cup powdered sugar
- 1 egg white
- 1/2 teaspoon vanilla extract
Pumpkin Cupcakes:
- 1 1/2 cups all-purpose flour
- 2 teaspoons pumpkin pie spice
- 1 1/2 teaspoons baking powder
- 1/2 teaspoon salt
- 1 cup pumpkin puree
- 1 cup sugar
- 2 eggs
- 1/2 cup vegetable oil
- 1 teaspoon vanilla extract
Brown Sugar Marshmallow Frosting:
- 4 egg whites
- 1 cup light brown sugar
- 1/2 teaspoon vanilla extract
Instructions
- Preheat the oven to 350ºF (175ºC). Line 18 muffin cups with paper liners.
- For the Filling: With an electric mixer, beat the softened cream cheese and the powdered sugar until light and fluffy, about 3 minutes. Add in the egg white and the vanilla extract and beat until just combined. Set aside.
- For the Cupcakes: In a medium bowl, whisk together the all-purpose flour, pumpkin pie spice, baking powder, and salt. In a separate large bowl, combine the pumpkin puree, sugar, eggs, vegetable oil, and vanilla extract. Gradually add the dry flour mixture to the wet pumpkin mixture, stirring gently until just combined. Be careful not to overmix.
- Assemble the Cupcakes: Put about 1 tablespoon of the pumpkin batter into each prepared muffin cup. Next, add a dollop (approximately 2 teaspoons) of the cheesecake mixture directly on top of the pumpkin batter. Finally, add another spoonful of pumpkin batter, dividing it evenly over the cheesecake filling, filling each cup about 2/3 full.
- Bake the cupcakes until they are golden brown and springy to the touch when gently pressed, about 20-25 minutes. Let cool completely on a wire rack before frosting.
- For the Brown Sugar Marshmallow Frosting: In the bowl of an electric mixer (preferably a stand mixer), combine the egg whites and light brown sugar. Place this bowl over a small pot containing about 1 inch of simmering water (creating a double boiler setup), ensuring the bottom of the mixer bowl does not touch the water. Whisk the mixture continuously until it registers 160ºF (71ºC) on an instant-read thermometer. This pasteurization step is important for safety.
- Carefully remove the bowl from the heat and return it to the electric mixer. Beat the mixture on high speed until it is very light, fluffy, and forms stiff, glossy peaks. This will take several minutes. Then, lower the speed to medium-low and continue to beat until the frosting cools down to room temperature, which typically takes about 5 minutes. Finally, beat in the 1/2 teaspoon of vanilla extract until fully incorporated.
- Pipe or spread the cooled brown sugar marshmallow frosting generously onto the completely cooled pumpkin cheesecake cupcakes. Serve and enjoy!
