Pumpkin cheesecake cupcakes pair a soft, spiced pumpkin cake with a creamy cheesecake center and a fluffy pumpkin spice buttercream, all in one handheld dessert.
Each cupcake hides a dollop of sweet cream cheese filling, and a sprinkle of graham cracker crumbs on top echoes a classic cheesecake crust. The recipe makes 12 cupcakes and suits fall potlucks, seasonal tables, and bake sales.
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Why This Pumpkin Cheesecake Cupcakes Recipe Works
Oil in the batter keeps the pumpkin cake moist for days, and pumpkin puree adds natural sweetness, color, and a tender crumb.
Spooning the cream cheese filling into the center before topping with more batter seals it inside. As the cupcakes bake, it turns into a creamy surprise in each bite.
The buttercream gets its flavor from a little pumpkin pie spice and vanilla, so it echoes the cake without hiding the cheesecake center.
Ingredients for Pumpkin Cheesecake Cupcakes
- 1 cup all purpose flour (for the cupcakes)
- 1 teaspoon pumpkin pie spice (for the cupcakes)
- 1 teaspoon baking powder
- 1/2 teaspoon ground cinnamon
- 1/2 teaspoon baking soda
- 1/4 teaspoon ground nutmeg
- 1/4 teaspoon salt
- 1 cup pumpkin puree (plain pumpkin, not pie filling)
- 1/2 cup granulated sugar (for the cupcakes)
- 1/3 cup packed brown sugar
- 1/2 cup vegetable oil
- 2 large eggs, at room temperature
- 4 oz cream cheese, at room temperature (for the filling)
- 1/3 cup granulated sugar (for the filling)
- 1/2 teaspoon pumpkin pie spice (for the filling)
- 1 cup unsalted butter, at room temperature (for the frosting)
- 3 cups powdered sugar (for the frosting)
- 2 tablespoons milk (for the frosting)
- 2 teaspoons vanilla extract (for the frosting)
- 1 teaspoon pumpkin pie spice (for the frosting)
- 1/2 cup graham cracker crumbs, for sprinkling
Pumpkin puree. Use plain canned pumpkin and blot it with a paper towel if it looks watery.
Pumpkin pie spice and cinnamon. The spice blend carries the fall flavor through the cake, filling, and frosting.
Vegetable oil. Oil gives a tender crumb and keeps the cupcakes soft.
Cream cheese. Soft cream cheese makes the filling smooth. Beat it until no lumps remain.
Unsalted butter. Butter at room temperature whips into a light frosting. It should dent when pressed but not look greasy.
Powdered sugar. Sift it if it is lumpy so the frosting turns out silky.
Graham cracker crumbs. They add a gentle crunch and a nod to a cheesecake crust.
How to Make Pumpkin Cheesecake Cupcakes
1. Prep the pan. Heat the oven to 350 degrees F and line a 12 cup muffin tin with paper liners.
2. Make the filling. Beat the cream cheese, 1/3 cup sugar, and 1/2 teaspoon pumpkin pie spice with a mixer for 2 to 3 minutes, until light and fluffy. Set aside.
3. Mix the dry ingredients. Whisk the flour, pumpkin pie spice, baking powder, cinnamon, baking soda, nutmeg, and salt in a large bowl.
4. Mix the wet ingredients. In another bowl, whisk the pumpkin puree, both sugars, oil, and eggs until smooth.
5. Combine. Pour the wet mixture over the dry and stir with a spatula just until moistened.
6. Fill the liners. Add a spoonful of batter to each liner, drop 2 teaspoons of filling in the center, and cover with the rest of the batter.
7. Bake. Bake for 15 to 18 minutes, until a toothpick inserted near the edge of the cake comes out clean. Cool completely on a wire rack before frosting.
8. Whip the frosting. Beat the butter and powdered sugar on medium for 1 to 2 minutes, then add the milk, vanilla, and pumpkin pie spice on low, and beat on medium high until fluffy.
9. Frost and top. Pipe or spread the frosting onto each cupcake and sprinkle with graham cracker crumbs.
How to Serve Pumpkin Cheesecake Cupcakes
Serve these cupcakes at room temperature for the ideal frosting texture. They fit right in on a fall dessert table with mini pumpkin bundt cakes, pumpkin doughnut muffins, and a slice of New York cheesecake. Add a tray of cinnamon streusel coffee cake for brunch.
How to Store and Reheat Pumpkin Cheesecake Cupcakes
Because of the cream cheese filling, store the frosted cupcakes in an airtight container in the refrigerator for 3 to 4 days. Let them sit at room temperature for about 20 minutes before serving so the frosting softens. For longer storage, freeze unfrosted cupcakes in a sealed container for up to three months, then thaw and frost.
Tips and Variations for Pumpkin Cheesecake Cupcakes
Use room temperature ingredients. Eggs, cream cheese, and butter blend more smoothly when they are not cold.
Measure the flour carefully. Spoon flour into the cup and level it so the cupcakes do not turn dry.
Do not overmix. Stir the batter just until it looks moist to keep the cupcakes tender.
Fill liners evenly. Use a cookie scoop for even cupcakes and an even cheesecake center.
Cool before frosting. Warm cupcakes melt buttercream, so wait until they are fully cooled.
Pipe or spread. A large star tip makes a bakery look, but an offset spatula works just as well.
Make a gluten free version. A gluten free flour blend can replace the all purpose flour.
Keep dairy cold. Refrigerate leftovers promptly. For general guidance on storing and reheating leftovers, see this guide from University of Minnesota Extension.
Frequently Asked Questions About Pumpkin Cheesecake Cupcakes
How do I know pumpkin cheesecake cupcakes are done?
A toothpick inserted into the cake near the edge should come out clean after 15 to 18 minutes.
Can I make pumpkin cheesecake cupcakes ahead of time?
Yes. Bake and freeze them unfrosted, or make them a day ahead and refrigerate once frosted.
Do pumpkin cheesecake cupcakes need to be refrigerated?
Yes. The cream cheese filling means they should be stored cold, then brought to room temperature before serving.
Can I use pumpkin pie filling instead of puree?
No. Pie filling is already sweetened and spiced, which changes the balance, so use plain puree.
Can I skip the frosting?
Yes. They are lovely with just the cheesecake center, but the frosting adds extra richness.
Pumpkin Cheesecake Cupcakes
Equipment
- 12-cup muffin tin
- paper liners
- Electric mixer
- Wire rack
- Piping bag with large star tip (optional)
Ingredients
Main Ingredients
- 1 cup all purpose flour for the cupcakes
- 1 tsp pumpkin pie spice for the cupcakes
- 1 tsp baking powder
- ½ tsp ground cinnamon
- ½ tsp baking soda
- ¼ tsp ground nutmeg
- ¼ tsp salt
- 1 cup pumpkin puree plain, not pie filling
- ½ cup granulated sugar for the cupcakes
- ⅓ cup brown sugar packed
- ½ cup vegetable oil
- 2 large eggs at room temperature
- 4 oz cream cheese at room temperature, for the filling
- ⅓ cup granulated sugar for the filling
- ½ tsp pumpkin pie spice for the filling
- 1 cup unsalted butter at room temperature, for the frosting
- 3 cup powdered sugar for the frosting
- 2 tbsp milk for the frosting
- 2 tsp vanilla extract for the frosting
- 1 tsp pumpkin pie spice for the frosting
- ½ cup graham cracker crumbs for sprinkling
Instructions
Cooking
- Prepare. Heat the oven to 350 degrees F and line a 12 cup muffin tin with paper liners. Filling. Beat the cream cheese, 1/3 cup sugar, and 1/2 teaspoon pumpkin pie spice until light and fluffy, 2 to 3 minutes. Set aside.
- Dry mix. Combine the flour, 1 teaspoon pumpkin pie spice, baking powder, cinnamon, baking soda, nutmeg, and salt. Wet mix. Whisk the pumpkin puree, both sugars, oil, and eggs.
- Batter. Pour the wet mix over the dry and stir until just moistened. Fill. Add a spoonful of batter to each liner, 2 teaspoons of filling in the center, then more batter on top.
- Bake. Bake 15 to 18 minutes until a toothpick near the edge comes out clean, then cool completely on a wire rack.
- Frosting. Beat the butter and powdered sugar 1 to 2 minutes, then beat in the milk, vanilla, and 1 teaspoon pumpkin pie spice until fluffy.
- Finish. Frost the cupcakes and sprinkle with graham cracker crumbs.
