Pumpkin Cheesecake Cupcakes are my most popular Fall dessert! They are light, fluffy, moist, and have the perfect balance of pumpkin and cheesecake. We top these delicious treats with generous swirls of snow-white cream cheese frosting, finished with a delicate dusting of cinnamon. This is no ordinary cupcake; it is a miniature monument to Fall’s most cherished flavors.
One bite of these is a moment of pure bliss. Your palate is first greeted by the frosting—a cool wave of tangy sweetness that is both luxurious and refreshing. Then, you sink into the heart of the cupcake itself. This is both light and velvety at the same time, combining pumpkin cake with cheesecake. This isn’t just a dessert; it’s the very essence of a cozy autumn day, melded into one perfect, elegant treat.
Pumpkin Cheesecake Cupcake Ingredients
Let’s take a closer look at the main ingredients that make up these delicious cupcakes.
Vegetable Oil
Vegetable oil adds moisture to the cupcakes evenly. Cupcakes made with this oil will also stay moister longer than those made with butter.
Pumpkin Puree
Pumpkin puree adds the delicious pumpkin flavor to the cake. Be sure you are using ‘canned pumpkin’ or ‘pumpkin puree’ and not ‘pumpkin pie filling.’ Pumpkin pie filling has added spices already mixed in which we do not want for this recipe. I love to use Libby’s Pumpkin Puree.
Eggs
Eggs give your cupcakes structure and serve as a binder.
Granulated Sugar
We use granulated sugar in this recipe to not only add sweetness but to tenderize as well. When sugar is added, it results in the flour and eggs forming weaker bonds which produces a more tender crumb.
Vanilla Extract
Vanilla extract acts as a flavor enhancer. I always use pure vanilla extract in my baking. It really elevates the quality of your baked goods.
Flour
I use King Arthur flour for all of my baking needs. (Not an affiliate – just really like their flour!) This specific all-purpose flour has a higher protein percentage (11.7%) than most other brands. A higher protein percentage equates to a stronger flour. All-purpose flour serves a wide variety of baking needs from cakes to pies to some breads.
Baking Soda and Baking Powder
Baking soda and baking powder serve as leavening agents.
Salt
Salt acts to enhance the flavor of the cupcakes, balancing the sweetness.
Spices
Cinnamon and nutmeg are the spices used to give these cupcakes their Fall flavors.
Why are Pumpkin Cheesecake Cupcakes the best Fall dessert?
Pumpkin Cheesecake Cupcakes are my most requested Fall recipe, hands down! There are a few reasons for this:
- You do not have to love pumpkin to love these cupcakes. I have friends that actually hate all things pumpkin and love these! The pumpkin adds a ton of moisture to the cupcakes while the cheesecake component adds creaminess, toning down the spice flavor.
- These cupcakes freeze beautifully making them super easy to have on hand for last minute homemade goodies.
- Having these in cupcake format instead of a cake means you can use them for multiple functions, cutting down on the time you have to spend in the kitchen.
- They are both simple and elegant and possess the quintessential Fall treat look!
How should I store Pumpkin Cheesecake Cupcakes?
Store covered cupcakes in the refrigerator for up to 5 days. Cupcakes may be frozen (with or without frosting) for up to 3 months. Freeze in an airtight container which is then wrapped in plastic wrap or aluminum foil. To thaw, let sit (still wrapped) in the refrigerator overnight.
Tips
- Measure correctly – I highly recommend using a kitchen scale when baking. Because baking measurements need to be exact, using a scale helps to measure as precisely as possible. It quite honestly was a complete game changer for me when I first started using one! I would be lost without it now.
- Room temperature is important! When certain ingredients (eggs, cream cheese, butter, etc.) are listed as room temperature, there are scientific reasons behind this. At room temperature, these ingredients blend together better and result in a smoother batter. Ultimately, you will end up with a better final product!
- Over-mixing – Take care to not over-mix the cupcake batter. When batter is mixed too much, it results in the gluten being activated. If this occurs, the cupcakes may be dense and chewy.
- Freezing – These cupcakes freeze perfectly, even with the frosting on and decorated. Freeze in an airtight container which is then wrapped in plastic wrap or aluminum foil. To thaw, let sit (still wrapped) in the refrigerator overnight.
My Preferred Tools
You may already have many of these items in your kitchen. I recommend the following for this recipe:
- Kitchen Scale – precisely measure ingredients
- Stand Mixer – to mix batter
- Cupcake Pan – to bake cupcakes
- Cooling Racks – to cool cupcakes and dishwasher friendly!!
- Wilton Decorating Kit – piping tips, bags, couplers, and more for decorating cupcakes
- Master Decorating Kit – ultimate cupcake decorating tip set
If you liked this recipe, try our
- Apple Spice Cake with Baked Apple Roses
- Pumpkin Cheesecake with Salted Caramel
- Pumpkin Cheesecake Swirl Bundt Cake
Pumpkin Cheesecake Cupcakes
Pumpkin Cheesecake Cupcakes are light, fluffy, moist, and have the perfect balance of pumpkin and cheesecake with a cream cheese frosting.

Ingredients
- CHEESECAKE FILLING:
- 1 (8 oz) pkg cream cheese, room temp
- ¼ cup (50 g) granulated sugar
- 1 tsp vanilla extract
- 1 egg, room temp
- PUMPKIN CUPCAKES:
- 1 (15 oz) can (2 cups) pumpkin puree
- 1 cup vegetable oil
- 4 eggs, room temp
- 2 tsp pure vanilla extract
- 1 ½ cups (297 g) granulated sugar
- 2 cups (240 g) all-purpose flour
- 2 tsp baking powder
- 1 tsp baking soda
- 1 ½ tsp cinnamon
- 1 tsp nutmeg
- 1 tsp salt
- CREAM CHEESE FROSTING:
- 8 oz (1 block) full-fat cream cheese
- ½ cup (1 stick) salted butter, softened
- 1 tsp pure vanilla extract
- 4 cups (480 g) confectioners’ sugar
- Pinch of salt
- TOPPING:
- Sprinkle of Cinnamon
Directions
- Step 1 PREP: Preheat oven to 350 degrees F. Line cupcake pans with 24 liners.
- Step 2 CHEESECAKE FILLING: Combine cream cheese, sugar, and vanilla in a bowl. Beat until smooth. Add egg and mix until just combined. Set aside.
- Step 3 PUMPKIN CUPCAKES: Mix pumpkin, oil, eggs, vanilla, and sugar in a large bowl. In a separate bowl, combine flour, baking powder, baking soda, cinnamon, nutmeg, and salt. Add to wet ingredients and stir just until mixed.
- Step 4 BAKE: Fill pans ½ full with batter, add a small scoop of cheesecake filling, and then top with pumpkin batter until almost full. Bake at 350 degrees F for 21-24 minutes or until toothpick inserted in middle has just a few moist crumbs. Remove from oven and transfer to a wire rack. Cool completely before frosting.
- Step 5 FROSTING: Beat together cream cheese and butter in a large bowl using a handheld or stand mixer until smooth, approximately 3 minutes. Add in confectioners’ sugar, salt, and vanilla. Beat on low until sugar is incorporated (about 1 minute) and then increase speed to medium and mix until fully combined. If frosting is too thick, add a little milk until you reach desired consistency. If too thin, add a bit more confectioners’ sugar or cornstarch, 1 Tbsp at a time. After frosting cupcakes, I add a sprinkle of cinnamon over the top of each.
- Step 6 STORAGE: Store covered cupcakes in the refrigerator for up to 5 days. Cupcakes may be frozen (with or without frosting) for up to 3 months. Freeze in an airtight container which is then wrapped in plastic wrap or aluminum foil. To thaw, let sit (still wrapped) in the refrigerator overnight.
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