These Pumpkin Cheesecake Cupcakes combine two of my favorites, pumpkin and cheesecake. They have amazing flavor, and the recipe is easy to make.

Once the fall weather hits, I love making all the Pumpkin Dessert Recipes. This recipe for mini pumpkin cheesecake cupcakes is one of my favorites. The cupcake recipe is made from scratch and then filled with cheesecake.
It is such a simple recipe as it combines two of my favorite flavors, pumpkin and cheesecake. Cupcakes are always a crowd favorite and perfect to serve for all your holiday dinners.
The cream cheese frosting really pulls all the flavors together and is easy to make. If you love making pumpkin recipes as much as we do, make this easy dessert for a crowd-pleasing treat. You will also love Easy Pumpkin Delight Recipe and Easy Pumpkin Cake Recipe. Let the kids help make Chocolate Acorns.
Table of contents
Why We Love This Cupcake Recipe
- Simple Ingredients – These cupcakes are made with simple ingredients. If you are a baker, you probably already have the majority of these ingredients. Stock up now for all your holiday baking.
- Single Serving Cupcakes – We love serving cupcakes especially when taking them to a holiday dinner. It makes it easy to serve and everyone loves to be able to grab and enjoy.
- Easy to Make – If you love the flavors of pumpkin and cheesecake. Then you are going to love these quick and easy cupcakes. We love that these cupcakes are made from scratch which makes them taste better.
Ingredients

Cupcakes
- All Purpose Flour. Spoon the flour into a measuring cup. Never scoop it because it isn’t measured as accurately.
- Baking Soda. You can try the Best Baking Soda Substitutes.
- Pumpkin Puree. Make sure to buy plain pumpkin puree and not pumpkin pie filling with spices.
- Brown Sugar. The Best Brown Sugar Substitutes.
Filling
- Cream Cheese. Softened at room temperature to make it easier to mix.
Frosting
- Unsalted Butter. I like to use unsalted to make the frosting and it’s easier to control the salt content.
- Powdered Sugar. Sift the powdered sugar so the frosting will be smooth.
- Vanilla Extract. Use pure vanilla extract. I also recommend using clear vanilla so the frosting color will not be altered.
Scroll to the bottom of the page and get the complete list of ingredients.
Variations and Substitutions
- Mini Cheesecakes – If you have a mini cupcake pan, make these cupcakes in this pan. This creates the perfect bite size dessert for the perfect treat to feed a crowd.
- Graham Cracker Crust – You can easily add a graham cracker crust with graham cracker crumbs and melted butter. It gives the cupcakes a delicious layer and an easy addition.
- Pumpkin Cupcakes – We love making these cupcakes from scratch. But if you prefer you can use a pumpkin cake mix to make the cupcake base. Then top with the cheesecake filling and the cream cheese topping. It will still be delicious and full of pumpkin flavor.
How to Make Pumpkin Cheesecake Cupcakes
- Step 1 – Heat the oven and prepare the pan. – Preheat the oven to 350 degrees Fahrenheit. Then line a cupcake pan with 12 cupcake liners.

Step 2. Combine the dry ingredients. In a large mixing bowl, whisk together the flour and pumpkin pie spice. Then add in the baking powder, cinnamon and salt.

Step 3. Use a separate bowl and combine the wet ingredients. Stir together the pumpkin puree and sugar. Add in brown sugar, vegetable oil and eggs.

Step 4. Mix Dry and Wet Ingredients until just combined.

Step 5. In a separate bowl, beat together the filling ingredients. I used an electric mixer.

Step 6. Pour batter into each cupcake tin. Then top each one with 2 teaspoons of the filling mixture.

Step 7. Then top with more pumpkin batter to cover the filling. Bake the cupcakes for 15-18 minutes or until a toothpick inserted in the pumpkin portion of the cupcakes comes out clean.

Step 8. While the cupcakes cool, make the frosting. Beat together the cream cheese and butter with a hand mixer or stand mixer until light and fluffy. We like to use the paddle attachment in a bowl of an electric mixer.

Step 9. Lower the speed on the mixer to low. Then gradually add in the powdered sugar until combined. Then mix in the vanilla extract.

Step 10. Combine until smooth.

Step 11. Once the cupcakes have cooled completely, pipe the frosting onto each cupcake.
Storage
Refrigerate the leftovers in an airtight container for up to 5 days.

Expert Tips
- Room Temperature Ingredients – When preparing these recipe, make sure to start with room temperature ingredients. The cream cheese blends with the other ingredients better which makes it smooth and creamy.
- Cupcake Liners – We recommend using cupcake liners in your muffin pan. This helps to easily fill the muffin tins with cupcake batter and easier to clean up. But you can still make this recipe if you do not have any cupcake liners.
- Pumpkin Puree – When making this recipe, make sure to use pumpkin puree and not pumpkin pie filling. The results will not be the same.
- Pumpkin Cupcakes – Adding the cheesecake filling is easy to do but dividing the pumpkin batter in half. This allows the cupcakes to have a delicious cheesecake filling in each bite.
- Frosting the Cupcakes – Before topping the cupcakes with the cream cheese frosting, make sure the cupcakes are completely cooled.
More Easy Pumpkin Dessert Recipes
If you are looking for a new dessert to try this fall, add this cupcake recipe for a crowd-pleasing dessert. Once you make it, come back and leave a star rating and comment please.
Pumpkin Cheesecake Cupcakes
Ingredients
For the Cupcakes:
- 1 cup All Purpose Flour
- 1 teaspoon Pumpkin Pie Spice
- 1 teaspoon Baking Powder
- 1/2 teaspoon Baking Soda
- 1/2 teaspoon Cinnamon
- 1/4 teaspoon Salt
- 1 cup Pumpkin Puree
- 1/2 cup Sugar
- 1/3 cup Brown Sugar
- 1/2 cup Vegetable Oil
- 2 Large Eggs
For the Filling:
- 4 ounces Cream Cheese softened
- 1/3 cup Sugar
- 1/2 teaspoon Pumpkin Pie Spice
For the Frosting:
- 8 ounces Cream Cheese softened
- 1/4 cup Butter
- 3 cups Powdered Sugar
- 1 teaspoon Vanilla Extract
Instructions
For the Cupcakes:
- Preheat the oven to 350 degrees Fahrenheit and line a cupcake pan with 12 cupcake liners.
- In a large mixing bowl, whisk together the flour, pumpkin pie spice, baking powder, cinnamon and salt. Set aside.
- In a separate mixing bowl, stir together the pumpkin puree, sugar, brown sugar, vegetable oil and eggs.
- Then stir the wet ingredients into the dry ingredients until just combined. Set aside.
- In a separate bowl, beat together the filling ingredients with a hand held mixer or stand up mixer.
- Pour a spoonful of the pumpkin batter into each cupcake tin. Top each one with 2 teaspoons of the filling mixture. Then top with more pumpkin batter to cover the filling.
- Bake for 15-18 minutes until a toothpick inserted in the pumpkin portion of the cupcakes comes out clean.
- Remove from the oven and allow the cupcakes to cool completely on wire racks while you prepare the frosting.
For the frosting:
- Beat together the cream cheese and butter with a hand held mixer or stand mixer until light and fluffy.
- Reduce the speed on the mixer to low and gradually add in the powdered sugar until combined and smooth.
- Then mix in the vanilla extract.
- Once the cupcakes have cooled completely at room temperature, pipe the frosting onto each cupcake. Serve and enjoy!