Healthy Pumpkin Cheesecakes are the perfect gluten free, low fat cheesecake treat! Made with greek yogurt, low in sugar and so delicious!

Healthy Pumpkin Cheesecakes on a white plate with a orange checked linen, pumpkin and cinnamon sticks off to the side.

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It’s no secret that we love ALL things pumpkin and healthier treats around here. From Healthy Pumpkin Muffins to Pumpkin Chicken Chili, and even these 30 Healthy Pumpkin Recipes – we’ve got LOTS of options when it comes to cooking with pumpkin.

A few weeks ago when I shared these Healthy Cheesecake Bites I knew they could easily be made into a delicious fall treat by adding pumpkin puree and a few more spices.

The result was delicious. 

Healthy Pumpkin Cheesecakes stacked on top of one another with a plate of cheesecakes in the background

These mini pumpkin cheesecakes are such a fun fall dessert. Perfect for sharing with friends, enjoying on football Sunday – or even making for a holiday treat!

Now, let’s get into what makes these cheesecakes ‘healthy’

What makes these cheesecakes better for you?

These cheesecakes are a lightened up version of the classic dessert you know and love. 

Lower in fat – A slice of cheesecake typically has about 30-40g of fat. These mini cheesecakes have 15g of fat per serving, which is almost half! The rich creaminess of yogurt helps to replace some of the cream cheese and make these much lighter.

Gluten/Grain Free- Cheesecake is often made with graham cracker crust – this recipe has almond flour for the base for all my gluten/grain free friends! (Although there is a substitution to make it with graham crackers)

Lower in sugar – Most cheesecakes have over 30g of sugar per slice. This recipe only has 14g of sugar. The filling is sweetened with maple syrup and there’s a tiny bit of brown sugar in the crust.

Ingredients for Healthy Cheesecakes

To make these mini healthier cheesecakes you’ll need: almond flour, neufchatel cream cheese, greek yogurt, vanilla extract, brown sugar, cinnamon, ginger, nutmeg, pumpkin puree, maple syrup, and melted butter. 

Ingredients for Healthy Pumpkin Cheesecakes in small white bowls: brown sugar, spices, almond flour, butter, pumpkin puree, maple syrup.

You’ll also need a muffin tin + silicone muffin liners. We like the silicone muffin liners the best because the cheesecakes pop right out of them. Foil liners will also work – but paper liners won’t as they will get stuck

How to make Healthier Cheesecake

It’s so simple to make these mini cheesecake bites! To make healthier cheesecakes, first mix together your crust.

Once your crust has combined, press into silicone muffin liners and bake until golden brown.

As crusts are baking – whip together filling until it is smooth and creamy.

A collage with step by step instructions showing how to make Healthy Pumpkin Cheesecakes

Scoop the filling into the baked crusts and place in the refrigerator for 6-8 hours until chilled.

When the cheesecakes have chilled, add fresh berries on top and serve.

Substitutions for healthy pumpkin cheesecakes:

We have included a few suggestions for this recipe below for you.

Room Temperature: It is very important that these ingredients are brought to room temperature for the smoothest filling. If you don’t, your filing won’t be as smooth. Cream cheese will leave little lumps if it’s not completely to room temp. This will still be fine for eating it, but not necessarily for presentation.  I think a fresh fruit garnish would be great with the “cookie” crumbs.

Baked: We don’t recommend baking these cheesecakes. In order to get a nice looking cheesecake with the Greek yogurt, you’d need to have a water bath in the oven and it’s overall a lot of work!

Coconut Flour: You can’t substitute coconut flour for almond flour. It doesn’t work with the cream cheese. The almond flour crumb mimics the graham crackers best.

Nut Free/ Graham Crackers: You can easily sub in 1 cup of finely ground graham crackers for almond flour. If you do this, we recommend taking out the brown sugar since those are sweet. I’d still add in the cinnamon if they are honey graham crackers. 

Sugar: We tried a honey infused crust to really try to mimic the classic graham cracker crust flavor but it just didn’t pop through. We also tried one with coconut sugar and did not like the taste. Brown sugar is the best choice here. It’s a ¼ cup over 10 mini cheesecakes which is a very minimal amount.

A close up of Healthy Pumpkin Cheesecakes on a white speckled plate

Dairy Free: We do not recommend any dairy free options for this recipe.

Maple SyrupWe haven’t tried swapping maple syrup for honey but I think it would work!

Neufchâtel Cream Cheese: This is just cream cheese with 1/3 less fat. Make sure to use the one in the block. Do not use any whipped versions. While I haven’t tested regular cream cheese in this recipe, I think it would work.

Muffin Liners: Foil or silicone muffin liners work best. Paper ones risk sticking and taking on too much moisture. 

Mix ins: I haven’t tried mixing anything into the filling of this (peanut butter, chocolate, berries, etc) but I think it would work. Alternatively, you can just top the cheesecakes with whatever garnish you like.

Making one large cheesecake: I haven’t tried making one large cheesecake with this recipe but I think it would work if you were to make it in a spring form cheesecake pan 

Crustless: I haven’t tried making these cheesecakes without the crust – but you could definitely just make the filling and serve it in a bowl as if it were pumpkin mousse.

A close up of a Gluten Free Pumpkin Cheesecake with a big bite taken out of it.

Serving Gluten Free Pumpkin Cheesecake:

These pumpkin cheesecakes are best made 24 hours in advance of when you have to serve them. They only need about 6 hours to cool, but if they can set in the refrigerator overnight they’ll be even better!

Serve chilled: These cheesecakes should be served chilled. They’re fine to sit out at room temp for 1-2 hours, but they will get soft, and they’re meant to be eaten cold.

With cinnamon: We served these with a sprinkle of cinnamon on top, but you could also do chocolate, peanut butter, caramel sauce really anything you like!

An overhead image of pumpkin cheesecakes on a grey background/in a plate

How to store Healthier Pumpkin Cheesecakes:

Cheesecake bites must be stored in the refrigerator. They will last in the refrigerator for up to 5 days. They can get a little moist on top from condensation in the refrigerator so I recommend just blotting them with a paper towel before serving if that happens

Freezing – You can freeze these cheesecakes. When ready to eat, just remove from the freezer and place in the refrigerator for 3-4 hours before enjoying, or pop in the microwave for 10-15 seconds until thawed and creamy.

A healthy pumpkin cheesecake with a bite taken out of it.

Other healthy dessert recipes we love:


Healthy Pumpkin Cheesecakes

Healthy Pumpkin Cheesecakes are the perfect gluten free, low fat cheesecake treat! Made with greek yogurt, low in sugar and so delicious!

Keyword healthy pumpkin cheesecake, pumpkin cheesecake
Total Time 6 hours 22 minutes
Servings 12 mini cheesecakes


  • Note: It is very important that these ingredients are brought to room temperature for the smoothest filling. If you don’t, your filing won’t be as smooth.

  • Preheat Oven to 350 Degrees

  • Stir together all crust ingredients until a coarse sand-like texture forms. Line a 12 cup muffin pan with foil or silicone muffin liners.

  • Press about 1.5 tablespoons of the crust mix into each of the 12 muffin cups. Depending on how fine your almond flour was, you might have some left over. Just distribute it evenly and cover the entire bottom of all the cups.

  • Bake for 11-12 minutes at 350 until the edges start to brown a tiny bit.

  • Remove crusts from the oven and allow the crust to cool while you prepare the filling. (You can put them in the refrigerator to cool quicker)

  • In the bowl of a stand mixer or with a hand mixer add all filling ingredients. Use your whisk attachment (if available otherwise regular beaters are fine) and whip the filling mixture on high speed for 5-6 minutes until everything is incorporated.

  • When your crust is completely cool, scoop 3 tablespoons of filling into each of the muffin cups.

  • You will be able to fill the cups ¾ of the way.

  • Put the cheesecakes into the fridge and chill for 6-8 hours or overnight.

Nutrition Facts

Nutrition Facts

Healthy Pumpkin Cheesecakes

Amount Per Serving (1 mini cheesecake)

Calories 168
Calories from Fat 99

% Daily Value*

Fat 11g17%

Saturated Fat 4g25%

Cholesterol 21mg7%

Sodium 128mg6%

Potassium 101mg3%

Carbohydrates 13g4%

Fiber 1g4%

Sugar 10g11%

Protein 5g10%

Vitamin A 1810IU36%

Vitamin C 1mg1%

Calcium 74mg7%

Iron 1mg6%

* Percent Daily Values are based on a 2000 calorie diet.



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