These Mini Pumpkin Cheesecakes are creamy with the perfect touch of spice. They taste like a complete indulgence, but they're actually healthy enough to enjoy for breakfast instead of just saving for dessert.

As I whip together cream cheese and pumpkin, I watch as the whirring beaters swirl white and orange together until they’re a creamy golden color.
The rich, heady aroma of warm spices hits my nose and with it, memories of holidays past waft through my mind.
Pumpkin pie, as well as apple, enrobed in flaky pastry, baking and making the whole house smell better than any bakery ever did.
Christmas carols humming on the radio or holiday specials playing on the TV in the background, although no one in particular seems to be watching.
If we’re lucky, snow falling softly, silently, beautifully. Each flake gracefully sashaying through the air, glimmering in the streetlight until it reaches its resting place.
Each and every family member together, talking, laughing, making memories.

These beautiful moments are to be cherished. These are the moments that make the daily grind of life worthwhile. The moments that give meaning to who we are.
These days I like to eat a bit healthier, even on the holidays, but by no means do I like to abstain from festivities. Nothing could be more festive than sitting down to a lovely holiday spread with your family. And to me, that includes dessert.
These little pumpkin cheesecakes are perfect for special occasions. You won’t feel deprived in the least. In fact, even family members who aren’t as conscious about eating healthy will enjoy them. Unless you read the recipe, you wouldn’t guess they’re actually full of healthy ingredients. They taste like a total indulgence.

The Best Healthy Mini Pumpkin Cheesecakes Recipe
Gluten Free Crust Ingredients
- Almond flour
- Arrowroot starch
- Coconut sugar
- Ground cinnamon
- Sea salt
- Coconut oil
- Vanilla extract
- Water
Pumpkin Filling Ingredients
- Cream cheese
- Coconut sugar
- Pumpkin puree
- Eggs
- Vanilla extract
- Cinnamon
- Nutmeg
- Ginger
- Cloves
- Sea salt

How to Make Mini Pumpkin Cheesecakes
- For the crust. Preheat the oven to 350F. Line a muffin tray with 12 paper liners. Whisk together the almond meal, arrowroot starch, coconut sugar, cinnamon, and salt in a large bowl. Add the coconut oil and vanilla and mix with a fork until it forms crumbles. Add the water a little at a time until the dough holds together when you squeeze it. Divide the dough between the 12 muffin wells and lightly press down. Bake 8 minutes.
- For the filling: Meanwhile, make the filling. To do so, beat together all ingredients until smooth.
- To assemble and bake: Once the crusts are pre-baked, spoon the filling on top. Put the trays into the oven and immediately turn the heat down to 325F. Bake until the cheesecakes are golden and starting to puff, about 25 minutes.
- To serve. Cool to room temperature, and then transfer to the fridge to chill, about 1 hour. Serve.
How to Store Mini Pumpkin Cheesecakes
Store these individual pumpkin cheesecakes wrapped in the fridge for up to 5 days.

Tips for Making Mini Pumpkin Cheesecake
- Cut the carbs. An easy way to cut the carbs for this recipe is to swap out the coconut sugar for your favorite type of keto brown sugar.
- Plan ahead. I think these little treats taste even better if the next day! If you can, make them a day before you want to serve them.
- Serve it up pretty. Right before serving, top each pumpkin cheesecake cupcake with a dollop of whipped cream (or coconut "whipped cream") and a sprinkle of ground cinnamon or nutmeg.

More Pumpkin Treats to Try


Mini Pumpkin Cheesecakes
- Total Time: 50 minutes
- Yield: 12 servings 1x
Description
These Mini Pumpkin Cheesecakes are creamy with the perfect touch of spice. They taste like a complete indulgence, but they're actually healthy enough to enjoy for breakfast instead of just saving for dessert.
Ingredients
Crust:
- 1 ¼ cups almond flour
- 2 tablespoons arrowroot starch
- 1 tablespoon coconut sugar
- ¼ teaspoon cinnamon
- ⅛ teaspoon sea salt
- 3 tablespoons coconut oil (melted)
- ¼ teaspoon pure vanilla extract
- 2 teaspoons water (or more as necessary)
Filling:
- 4 ounces cream cheese (softened slightly)
- ¼ cup coconut sugar
- ½ cup pumpkin puree
- 2 large eggs
- ½ teaspoon pure vanilla extract
- ¾ teaspoon cinnamon
- ¼ teaspoon nutmeg
- ¼ teaspoon dried ground ginger
- ⅛ teaspoon ground cloves
- 1 pinch sea salt
Instructions
For the Crust:
- Preheat the oven to 350F. Line a muffin tray with 12 paper liners.
- Whisk together the almond meal, arrowroot starch, coconut sugar, cinnamon, and salt in a large bowl. Add the coconut oil and vanilla and mix with a fork until it forms crumbles. Add the water a little at a time until the dough holds together when you squeeze it.
- Divide the dough between the 12 muffin wells and lightly press down. Bake 8 minutes.
For the Filling:
- Meanwhile, make the filling. To do so, beat together all ingredients until smooth.
To Assemble and Bake:
- Once the crusts are pre-baked, spoon the filling on top.
- Put the trays into the oven and immediately turn the heat down to 325F. Bake until the cheesecakes are golden and starting to puff, about 25 minutes.
To Serve:
- Cool to room temperature, and then transfer to the fridge to chill, about 1 hour.
- Serve.
Notes
- Net Carbs: 7g per serving (1 mini pumpkin cheesecake = 1 serving)
- Store these individual pumpkin cheesecakes wrapped in the fridge for up to 5 days.
- An easy way to cut the carbs for this recipe is to swap out the coconut sugar for your favorite type of keto brown sugar.
- If desired, right before serving, top each pumpkin cheesecake cupcake with a dollop of whipped cream (or coconut "whipped cream") and a sprinkle of ground cinnamon or nutmeg.
- Prep Time: 15 minutes
- Cook Time: 35 minutes
- Category: Dessert
- Cuisine: American
Nutrition
- Calories: 163
- Sugar: 4
- Sodium: 77
- Fat: 13
- Saturated Fat: 6
- Carbohydrates: 9
- Fiber: 2
- Protein: 4
- Cholesterol: 38
Keywords: Mini Pumpkin Cheesecakes, Pumpkin Cheesecake Cupcakes
This post was first published on Healthy Sweet Eats on November 19, 2015. It was updated with more information on November 22, 2021.
Bethany @ Athletic Avocado
I love mini-desserts, they are perfect when you eat a heavy meal but still want something sweet after!