These Mini Keto Pumpkin Cheesecakes are rich, creamy, and delicious, made with pumpkin puree and pumpkin pie spice. An easy low-carb treat for Halloween or Thanksgiving, with only 3 grams of net carbs each.

Fall is officially here, and I couldn’t wait to break out the pumpkin and share some fun recipes with you. I’ve been experimenting with different ideas, and I’m excited to bring you this delightful fall treat that’s sure to impress.
If you’re not in the mood to bake an entire keto pumpkin cheesecake or whip up a full keto pumpkin pie, these Mini Keto Pumpkin Cheesecakes are the perfect solution! They’re easy to make, require minimal prep time, and give you all the delicious flavors of pumpkin pie and cheesecake in individual portions.
Plus, they’re low-carb and ready in no time—perfect for when you’re craving a fall treat without the fuss of a full dessert.
Top them with my decadent keto caramel sauce for the best experience.
Why You’ll Love These Mini Pumpkin Cheesecakes
- Quicker to make than regular keto pumpkin cheesecake
- They are low carb and keto – One serving contains only 3 grams of net carbs!
- These cupcakes can be made ahead of time, which is great for meal prep or when expecting guests.
- Crowd-Pleaser: Everyone loves these cupcakes, making them a hit at social gatherings and family events.
- Festive: They’re perfect for holidays, especially Halloween, Thanksgiving, and Christmas, when pumpkin-flavored treats are especially popular.
Ingredients For Mini Pumpkin Cheesecakes
For these delicious low carb pumpkin cheesecake cupcakes, you need just a few simple ingredients that are cheap and very accessible:
For The Crust:
- Almond Flour – Almond flour is one of the best keto flours. It’s low-carb, packed with protein, healthy monounsaturated fats, and other essential nutrients like Vitamin E and Manganese. And most importantly, it works great as a flour substitute.
- Sweetener – When it comes to sweeteners, you can choose your favorite one. Mine are Erythritol, Swerve, Monk Fruit, or Allulose. For the crust, I used granular erythritol.
- Butter – Gives that great buttery flavor to the crust.
- Salt – Salt helps to balance the taste and keeps your muffins from becoming overly sugary.
For The Filling
- Cream Cheese – Softened, full-fat cream cheese is the secret to a creamy filling.
- Sweetener – for the filling, I use a powdered sweetener as it blends easily.
- Eggs – They act as a binder and soften the texture of our muffins.
- Vanilla Extract – For a boost of flavor.
- Pumpkin Puree – Make sure that your pumpkin puree (my favorite!) contains only one ingredient: Pumpkin. If you’re not sure which one to get, we are here to help you. Take a look at our guide on How to Roast Pumpkin and Make Pumpkin Puree.
- Pumpkin Pie Spice – The key is to use a mix that does not have any added sugar. Or you can try my homemade pumpkin pie spice.

How To Make Keto Pumpkin Cheesecakes
Following these simple steps, these almond flour pumpkin cheesecake cupcake bites will completely satisfy your sweet tooth and definitely impress your guests.
We’ll start by making the crust for our mini keto pumpkin cheesecakes:
In a mixing bowl, add the dry ingredients – the almond flour, sweetener, cinnamon (if using), and a pinch of salt. Pour the melted butter over the dry ingredients. Use a spatula or a wooden spoon to mix well until all of the dry ingredients are moistened by the butter and the mixture starts to come together.
Line a 12-cup muffin pan with parchment paper liners or use silicone muffin cups to prevent sticking. Evenly divide the crust mixture using a spoon or a cookie scoop.
Press down firmly on the mixture in each muffin cup to form a solid base for your cheesecakes. The back of a spoon or the bottom of a small glass can be used to press down evenly.
Bake them for about 5-8 minutes until it starts to brown.
Make The Filling
To make the cheesecake filling, you’ll want to start with cream cheese at room temperature. If your cream cheese is too cold, it will be lumpy, and mixing will not remove the lumps.
Mix all the ingredients in a bowl except the pumpkin.
Use 2/3 of the cream to fill the cupcake pan. Add pumpkin puree and pumpkin pie spice to the remaining cream cheese mixture and combine well.
Bake them until a toothpick can be poked into the center and come out cleanly for about 20-25 minutes.

Pro Tips
- Use Room Temperature Ingredients: This helps create a smoother, creamier filling.
- Avoid Overmixing: When making the cheesecake filling, mix at low to medium speed to avoid incorporating too much air. Too much air can cause the cupcakes to crack as they cool.
- Pure Pumpkin Puree: Make sure you’re using 100% pure pumpkin, not pumpkin pie filling, which contains added sugars.
- Don’t Overbake: Cheesecakes continue to set as they cool, so remove them from the oven when the centers are still slightly jiggly.

How To Store
- These Mini Cheesecakes can be stored nicely in the fridge for about a week. Simply place them in an airtight container and, if possible, towards the back of the refrigerator.
- If you want to freeze them, place the cupcakes on a clean plate, then wrap tightly with plastic wrap before placing them in a ziplock bag. Freeze for up to a month; any longer will cause the flavor and texture to deteriorate. When you want to eat them, make sure to take them out of the freezer a few hours before consuming them.

Looking For More Keto Pumpkin Recipes? Try these:

Easy Mini Keto Pumpkin Cheesecakes
Description
Ingredients
Crust
- 1 cup almond flour blanched, superfine
- 2 tbsp sweetener
- 4 tbsp unsalted butter melted
- 1/4 tsp cinnamon optional
- pinch of salt
Pumpkin Cheesecake Layer
- 16 oz cream cheese room temperature
- 1 cup powdered sweetener
- 2 large eggs room temperature
- 2 tsp pumpkin pie spice
- 1 tsp cinnamon
- 1/2 cup pumpkin puree
- 1 tsp pure vanilla extract
Instructions
- Preheat the oven to 350°F/180°C.
- Make the crust: In a large bowl, combine the almond flour, sweetener, melted butter, cinnamon, and a pinch of salt. Whisk together until well mixed.
- Line 16 muffin cups with muffin liners. Divide the crust mixture among the lined muffin cups, pressing about a tablespoon of the mixture firmly into the bottom of each cup.
- Bake the crusts in the preheated oven for 5-8 minutes, or until they are just starting to turn golden brown. Keep a close eye on them to prevent burning.
- Make the filling: In a large mixing bowl, use an electric mixer to blend the cream cheese, powdered sweetener, eggs, vanilla extract, pumpkin pie spice, and cinnamon until smooth and creamy.
- Take 1/3 of the cheesecake filling and mix it with the pumpkin puree until well combined.
- Pour the cheesecake filling over each cooked crust, then top with a tablespoon of the pumpkin mixture.
- Bake for 20-25 minutes, or until the tops are nearly set but still slightly soft in the center.
- Remove from the oven and let them cool at room temperature. Once cooled, refrigerate the cheesecakes for at least 2 hours to allow them to set completely.
- Serve with homemade keto caramel sauce and a pinch of sea salt. Whipped cream or candied pecans are great toppings too.
Notes
How do we calculate the nutrition info?
These nutrition facts listed are determined using nutrition information from the USDA Food Database. Our nutrition facts are accurate, but if you are using different products, please make your calculations. Net carb count is calculated by subtracting both fiber and sugar alcohols because they don’t raise blood sugar.



