Pumpkin Cheesecake Cupcake Recipe tastes like a cozy slice of pumpkin pie and creamy cheesecake tucked into one handheld bite, perfect for fall cravings or honestly any random Tuesday, and it takes about 1 hour total from start to finish, including baking and cooling time. This dessert works well for holiday parties, potlucks, bake sales, or those nights when you want something impressive without wrestling a springform pan. I tested this recipe on my neighbors before sharing it here, and they now “accidentally” walk by my house whenever they smell pumpkin spice in the oven.
Why Make This Pumpkin Cheesecake Cupcake Recipe at Home
You get the best parts of pumpkin pie and cheesecake in a cupcake wrapper, which means no tricky water baths and no slicing drama. The texture hits that sweet spot: tender pumpkin cake on the outside with a rich, tangy cheesecake center that stays creamy but not runny.
Homemade pumpkin cheesecake cupcakes also let you control sweetness, spice level, and portion size. You can use pantry staples, skip weird preservatives, and customize the topping with whipped cream, caramel, or a simple dusting of cinnamon sugar.
“These pumpkin cheesecake cupcakes taste like a bakery special, but my kids thought I picked them up at a fancy shop instead of making them at home. ★★★★★”
Ingredients You Need
Pumpkin cupcake base
- 1 cup canned pumpkin puree
- Use 100% pumpkin, not pumpkin pie filling. Libby’s or store brand both work.
- 2 large eggs, room temperature
- 1/2 cup granulated sugar
- 1/2 cup light brown sugar, packed
- 1/2 cup neutral oil
- Vegetable, canola, or light olive oil all work.
- 1 teaspoon vanilla extract
- 1 cup all-purpose flour
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 1/2 teaspoon fine sea salt
- 1 1/2 teaspoons ground cinnamon
- 1/2 teaspoon ground ginger
- 1/4 teaspoon ground nutmeg
- 1/8 teaspoon ground cloves
- You can swap the individual spices for 2 teaspoons pumpkin pie spice if that sits in your pantry already.
Cheesecake filling
- 8 ounces cream cheese, softened
- Use full-fat brick style for best texture; avoid whipped tubs.
- 1/3 cup granulated sugar
- 1 large egg yolk
- 1 teaspoon vanilla extract
- 1 tablespoon sour cream or plain Greek yogurt
- This adds tang and helps the center stay creamy.
Optional topping
- Lightly sweetened whipped cream or canned whipped topping
- Ground cinnamon or pumpkin pie spice for dusting
- Caramel sauce or chocolate drizzle, if you like extra sweetness
Equipment
- 12-cup muffin tin
- Paper cupcake liners
- Two mixing bowls
- Hand mixer or stand mixer
- Rubber spatula
- Cookie scoop or tablespoon measure
- Toothpick for doneness testing
- Wire cooling rack
Tips & Mistakes
- Use room temperature cream cheese so the cheesecake filling turns smooth and lump free.
- Whisk the dry ingredients separately so you avoid pockets of baking soda or spices in the cupcakes.
- Mix the pumpkin batter just until combined to keep the texture soft and tender.
- Do not overfill the cupcake liners; aim for about one heaping tablespoon of pumpkin batter on the bottom and another on top.
- Keep the cheesecake filling in the center and avoid touching the sides of the liner to prevent sticking.
- Bake on the middle rack so the tops do not brown too quickly while the centers still set.
- Pull the cupcakes out when the edges look set and a toothpick near the edge comes out with a few moist crumbs, not dry.
- Cool the cupcakes completely before chilling so condensation does not make the tops soggy.
- Chill at least 2 hours so the cheesecake centers firm up and slice cleanly when you bite in.
- Skip warm storage; always refrigerate these since they contain cream cheese.
How to Make Pumpkin Cheesecake Cupcake Recipe
Step 1: Prep the pan and oven
Preheat your oven to 350°F. Line a 12-cup muffin pan with paper liners so the cupcakes release easily and stay neat. Set the pan aside while you mix the fillings.
Step 2: Mix the cheesecake filling
In a medium bowl, beat the softened cream cheese with a hand mixer until smooth and fluffy. Add the sugar, egg yolk, vanilla, and sour cream. Beat again until the mixture turns silky and thick, scraping the bowl as needed.
Taste a tiny bit to check sweetness and adjust with another teaspoon of sugar if you prefer a sweeter center. Set the cheesecake filling aside while you make the pumpkin batter.
Step 3: Stir together dry ingredients
In a separate bowl, whisk the flour, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves. Make sure the spices distribute evenly so every cupcake tastes balanced. Keep this bowl nearby.
Step 4: Mix the pumpkin batter
In a large bowl, whisk the pumpkin puree, granulated sugar, brown sugar, oil, eggs, and vanilla until smooth and glossy. Sprinkle the dry mixture over the wet mixture. Gently fold everything together with a spatula until no dry streaks of flour remain.
Stop mixing as soon as the batter looks uniform so you avoid tough cupcakes. The batter should look thick but scoopable.
Step 5: Fill the cupcake liners
Scoop about 1 heaping tablespoon of pumpkin batter into each cupcake liner. Add about 1 tablespoon of cheesecake filling in the center of each cup. Top each one with another tablespoon of pumpkin batter, covering the cheesecake filling completely.
Smooth the tops lightly with the back of a spoon if needed. The liners should look about two-thirds to three-quarters full.
Step 6: Bake
Place the muffin pan on the middle rack of the preheated oven. Bake for 18 to 22 minutes, depending on your oven. Check around 18 minutes by inserting a toothpick near the outer edge of a cupcake.
You want the toothpick to come out with a few moist crumbs but no wet batter. The centers may look slightly soft because of the cheesecake, but they should not jiggle like liquid.
Step 7: Cool and chill
Let the cupcakes cool in the pan for 10 minutes. Transfer them to a wire rack and cool completely at room temperature. Move the cooled cupcakes to the fridge and chill at least 2 hours before serving.
Chilling allows the cheesecake center to firm up and the flavors to deepen. You can chill them overnight if you plan to serve them the next day.
Step 8: Add toppings and serve
Right before serving, top each pumpkin cheesecake cupcake with a swirl of whipped cream. Dust lightly with cinnamon or pumpkin pie spice. Add a drizzle of caramel or chocolate if you want extra flair.
Serve chilled or slightly cool for the best texture.
Variations I've Tried
I swapped the regular cream cheese for flavored pumpkin spice cream cheese once, and the cupcakes tasted extra rich and autumn-forward. I also used chocolate chips in the pumpkin batter, which gave a nice texture contrast and a mocha vibe. A streusel topping with brown sugar, flour, cinnamon, and cold butter added a bakery-style crunch on top.
I tested a gluten free version using a 1:1 gluten free baking flour, and the cupcakes still turned out soft and moist. I also used coconut sugar in place of brown sugar in one batch, which added a mild caramel flavor and slightly darker color. Mini versions in a mini muffin tin worked well too; I just shortened the bake time to about 11 to 13 minutes.
How to Serve Pumpkin Cheesecake Cupcake Recipe
Serve pumpkin cheesecake cupcakes chilled or slightly cool so the cheesecake center feels creamy and lush. Add a swirl of whipped cream and a sprinkle of cinnamon for a simple finish that looks bakery-level. Pair them with hot coffee, chai, spiced tea, or a cold glass of milk for a cozy treat. These cupcakes also sit nicely on a holiday dessert table next to classic pumpkin pie, so guests can pick their favorite style of pumpkin dessert.
How to store
- Store pumpkin cheesecake cupcakes in an airtight container in the fridge for up to 4 days.
- Chill the cupcakes completely before covering them so condensation does not make the tops soggy.
- Freeze unfrosted cupcakes on a baking sheet until firm, then move them to a freezer bag or container for up to 2 months.
- Thaw frozen cupcakes in the fridge overnight, then add whipped cream or toppings right before serving.
- Reheat gently in the microwave for 5 to 10 seconds if you want them slightly warmer, but keep them cool enough so the cheesecake center stays firm.
Pumpkin Cheesecake Cupcake Recipe
Ingredients
Method
- Preheat the oven to 350°F (175°C). Line a 12-cup muffin pan with paper cupcake liners and set aside.
- Make the cheesecake filling: In a medium bowl, beat the softened cream cheese with a hand mixer until smooth and fluffy. Add the granulated sugar, egg yolk, vanilla, and sour cream or Greek yogurt. Beat until silky and thick, scraping down the bowl as needed. Set aside.
- In a separate bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves until the spices are evenly distributed.
- In a large bowl, whisk the pumpkin puree, granulated sugar, brown sugar, oil, eggs, and vanilla until smooth and glossy. Sprinkle the dry ingredients over the wet ingredients and gently fold with a spatula just until no dry flour remains.
- Fill the cupcake liners: Spoon about 1 heaping tablespoon of pumpkin batter into the bottom of each liner. Add about 1 tablespoon of cheesecake filling in the center of each, keeping it away from the sides. Cover with another tablespoon of pumpkin batter so the cheesecake filling is completely enclosed. The liners should be about two-thirds to three-quarters full.
- Bake on the middle rack for 18 to 22 minutes, until the edges look set and a toothpick inserted near the outer edge of a cupcake comes out with a few moist crumbs but no wet batter. The centers may look slightly soft but should not jiggle like liquid.
- Cool the cupcakes in the pan for 10 minutes, then transfer to a wire rack to cool completely. Once cooled, refrigerate for at least 2 hours, or until the cheesecake centers are fully chilled and set.
- Just before serving, top each cupcake with a swirl of whipped cream, a light dusting of cinnamon or pumpkin pie spice, and a drizzle of caramel or chocolate if desired. Serve chilled or slightly cool.
Notes
Approximate per 1 cupcake (1 of 12), without optional toppings: 260–290 calories; fat 16 g; saturated fat 6 g; carbohydrates 29 g; fiber 1 g; sugars 21 g; protein 4 g; sodium 220 mg. Values are estimates and will vary based on specific ingredients, brands, and portion sizes.