
These mini pumpkin cheesecakes transform a classic dessert into perfect individual portions filled with warm autumn spices and creamy pumpkin goodness. They balance rich cream cheese with seasonal pumpkin flavors for an irresistible fall treat that's easier to make than a full-sized cheesecake.
I first made these for a Thanksgiving gathering when I wanted something more special than pumpkin pie but less fussy than a full cheesecake. My family now requests them for every autumn celebration, and they've become our signature holiday dessert.
Ingredients
- Graham cracker crumbs: Form the perfect crunchy base that contrasts with the creamy filling. Look for boxes of premade crumbs or process whole crackers yourself for the freshest flavor.
- Cream cheese: Provides the signature tangy richness. Use full-fat Philadelphia brand for the creamiest texture and allow it to come fully to room temperature.
- Pumpkin puree: Brings seasonal flavor and color. Choose 100% pure pumpkin not pumpkin pie filling which contains additives and sweeteners.
- Brown sugar: Adds depth with its molasses notes that complement the pumpkin beautifully. Light or dark varieties work equally well.
- Warming spices: Cinnamon, nutmeg, and ginger create that classic pumpkin spice profile. Freshly grated nutmeg makes a noticeable difference.
- Vanilla extract: Enhances all the other flavors. Use pure extract rather than imitation for best results.
Step-by-Step Instructions
- Prepare the Pans:
- Preheat your oven to 350°F and line 24 regular muffin cups with paper liners. The liners make removal easy and help maintain the cheesecakes' shape.
- Create the Graham Cracker Base:
- In a medium bowl thoroughly combine the graham cracker crumbs with both sugars until evenly mixed then pour in the melted butter. The mixture should look like wet sand and hold together when pressed. Divide this mixture among your prepared muffin cups using about 1½ tablespoons per cup then press firmly with the bottom of a small glass or measuring cup. The firmer you press the better your crust will hold together. Place in refrigerator while preparing the filling.
- Mix the Pumpkin Base:
- In a large bowl combine the pumpkin puree, eggs, brown sugar, and all spices. Beat until completely smooth making sure to scrape down the sides of the bowl. The mixture should have a consistent color with no streaks of spice visible.
- Prepare the Cream Cheese Mixture:
- In a separate bowl beat the softened cream cheese with granulated sugar and vanilla until completely smooth and fluffy. Take your time with this step as any lumps now will remain in the final product. The mixture should be light and creamy with no visible chunks of cream cheese.
- Combine the Fillings:
- Gradually add the pumpkin mixture to the cream cheese mixture blending thoroughly after each addition. Continue mixing until the batter has a uniform color and texture with no streaks. This creates the perfect balance of pumpkin flavor and cheesecake richness.
- Fill and Bake:
- Using a measuring cup or ice cream scoop portion approximately ⅓ cup of filling into each crust-lined muffin cup. The cups should be nearly full. Bake in your preheated oven for 25-30 minutes until the centers are just set but still have a slight jiggle.
- Cool and Chill:
- Allow the cheesecakes to cool completely on a wire rack then refrigerate covered for at least 2-3 hours or overnight. This chilling time is essential for the cheesecakes to fully set and develop their flavor.

The warm spices in this recipe always remind me of my grandmother's kitchen during the holidays. She taught me that using fresh spices makes all the difference, especially freshly grated nutmeg which adds an aromatic quality that the pre-ground version just can't match. Whenever I make these, the scent filling my kitchen brings me right back to those special family gatherings.
Serving Suggestions
These mini cheesecakes stand beautifully on their own, but for special occasions, I love to add a dollop of freshly whipped cream and a sprinkle of cinnamon or crushed graham crackers on top. For an extra decadent touch, drizzle with caramel sauce or add a pecan half to each one. They pair wonderfully with a cup of coffee or spiced apple cider, making them perfect for an autumn dessert table or afternoon tea.
Storage Tips
These mini pumpkin cheesecakes keep beautifully in the refrigerator for up to 5 days. Store them in an airtight container, separating layers with parchment paper to prevent sticking. For longer storage, freeze the completely cooled cheesecakes on a baking sheet until solid, then transfer to a freezer-safe container with parchment between layers. When ready to enjoy, thaw overnight in the refrigerator or for about 2 hours at room temperature.
Troubleshooting Tips
If your cheesecakes develop cracks during baking, you may have overmixed the batter introducing too much air. Next time, mix just until ingredients are combined. Small cracks can easily be covered with whipped cream or a fruit topping. If your cheesecakes sink in the middle after cooling, they likely needed a few more minutes in the oven. The centers should be just set but still have a slight jiggle when done. The toothpick test doesn't work well for cheesecakes.

Frequently Asked Questions
- → Can I make these mini pumpkin cheesecakes ahead of time?
Yes! These mini pumpkin cheesecakes actually benefit from being made ahead. They need 2-3 hours of refrigeration after baking, but can be made up to 2 days in advance. Store them covered in the refrigerator until ready to serve.
- → Can I use pumpkin pie filling instead of pumpkin puree?
It's not recommended to substitute pumpkin pie filling for puree in this recipe. Pumpkin pie filling already contains sugar and spices, which would alter the flavor balance of the cheesecakes. Stick with plain pumpkin puree for best results.
- → How do I know when the mini cheesecakes are done baking?
The mini cheesecakes are done when the centers are set but still slightly jiggly. They should not be liquid in the middle, but shouldn't be completely firm either. They'll continue to set as they cool.
- → Can I freeze these mini pumpkin cheesecakes?
Yes, these freeze beautifully! Once completely cooled, place them in an airtight container with parchment between layers and freeze for up to 2 months. Thaw overnight in the refrigerator before serving.
- → What toppings go well with mini pumpkin cheesecakes?
These mini cheesecakes are delicious as is, but can be enhanced with whipped cream, a sprinkle of cinnamon, crushed graham crackers, caramel sauce, or chopped pecans. For special occasions, a small candied pumpkin decoration makes them festive.
- → Can I make these without a muffin tin?
While a muffin tin is ideal for creating the perfect individual portions, you could adapt this recipe to make in a mini cheesecake pan with removable bottoms. Alternatively, you could make one large cheesecake, but would need to adjust baking time considerably.