Remember those crisp autumn days, the scent of cinnamon and nutmeg drifting from the kitchen, and the comforting feeling of cozying up with a delicious treat? There’s something truly magical about the fall season, and for many of us, it evokes memories of warmth, family, and, of course, incredible desserts. Today, we share a recipe that encapsulates all that autumnal charm and more: our exquisite Pumpkin Cheesecake Filled Cupcakes. Get ready to embark on a culinary journey that combines the best of two beloved desserts into one delightful bite-sized wonder. These are not just cupcakes; they are a little piece of edible happiness, designed to bring joy and a touch of seasonal magic to your home.
Why Make This Recipe
Experience the harmonious blend of moist pumpkin spice cupcake and creamy, tangy cheesecake filling in every single bite. It’s a dessert mashup you never knew you needed! These cupcakes are infused with classic autumn spices like cinnamon, nutmeg, and ginger, making them perfect for holiday gatherings or a cozy evening in. While they look sophisticated, our step-by-step guide makes creating these stunning Pumpkin Cheesecake Filled Cupcakes surprisingly simple, even for novice bakers. Whether you are hosting a dinner party or simply treating your family, these delightful cupcakes are guaranteed to be a hit. They are perfect for Thanksgiving, Halloween parties, autumn potlucks, or simply as a comforting weekend bake.
How to Make Pumpkin Cheesecake Filled Cupcakes
You will make the pumpkin cupcakes first, then the cheesecake filling. After the cupcakes cool, you will core them and fill them with the creamy cheesecake. Finally, you can add a delicious cream cheese frosting.
Ingredients of Pumpkin Cheesecake Filled Cupcakes
#### For the Pumpkin Cupcakes:
- Dry Ingredients:
- 1 ½ cups All-purpose flour
- 1 cup Granulated sugar
- ½ cup Brown sugar (packed)
- 2 teaspoons Baking powder
- 1 teaspoon Baking soda
- ½ teaspoon Salt
- 1 teaspoon Ground cinnamon
- ½ teaspoon Ground nutmeg
- ½ teaspoon Ground ginger
- ¼ teaspoon Ground cloves (optional)
- Wet Ingredients:
- 1 cup Canned pumpkin puree (not pumpkin pie filling)
- 2 Large eggs
- ½ cup Vegetable oil or melted unsalted butter
- ¼ cup Milk
#### For the Cheesecake Filling:
- 8 ounces Cream cheese, softened
- ¼ cup Granulated sugar
- 1 Large egg yolk
- 1 teaspoon Vanilla extract
- Pinch of salt
#### For the Cream Cheese Frosting (Optional but Highly Recommended):
- ½ cup Unsalted butter, softened
- 8 ounces Cream cheese, softened
- 3-4 cups Powdered sugar (confectioners’ sugar)
- 1 teaspoon Vanilla extract
- Pinch of salt
Directions of Pumpkin Cheesecake Filled Cupcakes
#### Step 1: Prepare the Pumpkin Cupcakes
- Preheat & Prep: Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
- Combine Dry Ingredients: In a large bowl, whisk together the flour, granulated sugar, brown sugar, baking powder, baking soda, salt, cinnamon, nutmeg, ginger, and cloves (if using).
- Mix Wet Ingredients: In a separate medium bowl, whisk together the pumpkin puree, eggs, oil (or melted butter), and milk until well combined.
- Combine Wet and Dry: Pour the wet ingredients into the dry ingredients and mix until just combined. Do not overmix!
- Fill Liners & Bake: Divide the batter evenly among the prepared muffin cups, filling each about two-thirds full. Bake for 18-22 minutes, or until a toothpick inserted into the center comes out clean.
- Cool: Let the cupcakes cool in the muffin tin for 5 minutes before transferring them to a wire rack to cool completely.
#### Step 2: Make the Cheesecake Filling
- Cream Ingredients: In a medium bowl, beat the softened cream cheese and granulated sugar together until smooth and creamy.
- Add Remaining Ingredients: Beat in the egg yolk, vanilla extract, and a pinch of salt until just combined. Set aside.
#### Step 3: Fill the Cupcakes
- Create a Cavity: Once the pumpkin cupcakes are completely cooled, use a small paring knife or a cupcake corer to carefully remove a small cone from the center of each cupcake. Do not go all the way through!
- Fill with Cheesecake: Spoon or pipe the cheesecake filling into each cavity. You can use the removed cupcake piece to place back on top of the filling, or simply leave it open for frosting.
#### Step 4: Prepare and Pipe the Cream Cheese Frosting (Optional)
- Beat Butter & Cream Cheese: In a large bowl, beat the softened butter and softened cream cheese together until light and fluffy.
- Add Sugar & Vanilla: Gradually add the powdered sugar, one cup at a time, beating until smooth. Stir in the vanilla extract and salt.
- Frost: Once the Pumpkin Cheesecake Filled Cupcakes are filled, pipe or spread a generous dollop of cream cheese frosting on top of each cupcake.
How to Serve Pumpkin Cheesecake Filled Cupcakes
Serve individual Pumpkin Cheesecake Filled Cupcakes with a dusting of cinnamon or a sprinkle of chopped pecans. These cupcakes are the perfect accompaniment to a warm cup of coffee, chai latte, or spiced apple cider. Arrange these elegant treats on a platter for a beautiful addition to any fall gathering or holiday spread.
How to Store Pumpkin Cheesecake Filled Cupcakes
Store Pumpkin Cheesecake Filled Cupcakes in an airtight container in the refrigerator for up to 3-4 days.
Tips to Make Pumpkin Cheesecake Filled Cupcakes
- Room Temperature Ingredients: Ensure your cream cheese, butter, and eggs are at room temperature for the smoothest batter and frosting.
- Do Not Overmix: Overmixing the cupcake batter can lead to tough cupcakes. Mix until just combined.
- Cool Completely: It is crucial that the cupcakes are completely cool before filling, otherwise the cheesecake filling will melt.
- Measure Accurately: Baking is a science! Use proper measuring techniques for consistent results.
- Do Not Overbake: Keep an eye on the cupcakes; overbaking can lead to dry results. The toothpick test is your best friend.
- Chill the Filling: If your cheesecake filling seems too soft, a quick chill in the refrigerator can help it firm up for easier handling.
- Invest in a Corer: A cupcake corer makes creating the cavity for the cheesecake filling much easier and neater.
Variation
- Pecan Streusel Topping: Add a crunchy pecan streusel to the top of your cupcakes before baking for an extra layer of texture and flavor.
- Caramel Drizzle: A drizzle of homemade or store-bought caramel sauce on top of the cream cheese frosting takes these over the top.
- Spiced Whipped Cream: For a lighter topping, consider a dollop of spiced whipped cream instead of cream cheese frosting.
- Chocolate Chip Integration: Fold in a handful of mini chocolate chips into the pumpkin cupcake batter for a delightful twist.
FAQs
Q1: Can I make these Pumpkin Cheesecake Filled Cupcakes ahead of time?
Yes, you can! You can bake the pumpkin cupcakes and prepare the cheesecake filling a day in advance. Store the cooled cupcakes in an airtight container at room temperature, and keep the cheesecake filling refrigerated. Fill and frost just before serving for the freshest taste.
Q2: What’s the difference between pumpkin puree and pumpkin pie filling?
It is crucial to use plain canned pumpkin puree for these Pumpkin Cheesecake Filled Cupcakes, not pumpkin pie filling. Pumpkin pie filling is already spiced and sweetened, which would alter the flavor profile of this recipe.
Q3: My cheesecake filling seems a bit thin; what can I do?
If your cheesecake filling seems a bit too loose, try chilling it in the refrigerator for 20-30 minutes. This will help it firm up, making it easier to pipe or spoon into your Pumpkin Cheesecake Filled Cupcakes.

Classic Pumpkin Cheesecake Filled Cupcakes
Equipment
- Muffin tin
- Paper liners
- Large bowl
- Whisk
- Medium bowl
- Wire rack
- Small paring knife
- Cupcake corer
- Spoon
- Pipe
Ingredients
For the Pumpkin Cupcakes:
- 1 ½ cups All-purpose flour
- 1 cup Granulated sugar
- ½ cup Brown sugar packed
- 2 teaspoons Baking powder
- 1 teaspoon Baking soda
- ½ teaspoon Salt
- 1 teaspoon Ground cinnamon
- ½ teaspoon Ground nutmeg
- ½ teaspoon Ground ginger
- ¼ teaspoon Ground cloves optional
- 1 cup Canned pumpkin puree not pumpkin pie filling
- 2 Large eggs
- ½ cup Vegetable oil or melted unsalted butter
- ¼ cup Milk
For the Cheesecake Filling:
- 8 ounces Cream cheese softened
- ¼ cup Granulated sugar
- 1 Large egg yolk
- 1 teaspoon Vanilla extract
- Salt Pinch of
For the Cream Cheese Frosting (Optional but Highly Recommended):
- ½ cup Unsalted butter softened
- 8 ounces Cream cheese softened
- 3-4 cups Powdered sugar confectioners' sugar
- 1 teaspoon Vanilla extract
- Salt Pinch of
Instructions
Prepare the Pumpkin Cupcakes:
- Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
- In a large bowl, whisk together the flour, sugars, baking powder, baking soda, salt, cinnamon, nutmeg, ginger, and cloves.
- In a separate medium bowl, whisk together the pumpkin puree, eggs, oil (or melted butter), and milk until well combined.
- Pour the wet ingredients into the dry ingredients and mix until just combined, ensuring not to overmix.
- Divide the batter evenly among the prepared muffin cups, filling each about two-thirds full, then bake for 18-22 minutes, or until a toothpick inserted into the center comes out clean.
- Let the cupcakes cool in the muffin tin for 5 minutes before transferring them to a wire rack to cool completely.
Make the Cheesecake Filling:
- In a medium bowl, beat the softened cream cheese and granulated sugar together until smooth and creamy.
- Beat in the egg yolk, vanilla extract, and a pinch of salt until just combined, then set aside.
Fill the Cupcakes:
- Once the pumpkin cupcakes are completely cooled, use a small paring knife or a cupcake corer to carefully remove a small cone from the center of each cupcake, ensuring not to go all the way through.
- Spoon or pipe the cheesecake filling into each cavity; you can use the removed cupcake piece to place back on top of the filling, or simply leave it open for frosting.
Prepare and Pipe the Cream Cheese Frosting (Optional):
- In a large bowl, beat the softened butter and softened cream cheese together until light and fluffy.
- Gradually add the powdered sugar, one cup at a time, beating until smooth, then stir in the vanilla extract and salt.
- Once the Pumpkin Cheesecake Filled Cupcakes are filled, pipe or spread a generous dollop of cream cheese frosting on top of each cupcake.