Skinny Mini Pumpkin Cheesecakes filled with pumpkin puree and pumpkin spice, complete with a crust made of chopped pecans and maple syrup. Made “mini” size, so there’s no messy cutting or long bake times; these are a great, healthier Holiday dessert, made gluten-free, grain-free, and refined sugar-free.
The last recipe I posted, I shared an easy cookie recipe for the Holidays.
In that post, I promised there would be more desserts coming your way that were perfect for the Holidays. That are a little more “fancy,” for those of you who like to kick your entertaining up a notch or two 🙂
I like having the best of both worlds, so my favorite thing is to have at least two different desserts at Thanksgiving and Christmas. One dessert can be more casual, like Cranberry Coconut Oatmeal Cookies. While the other can be a little more “fancy,” like these Skinny Mini Pumpkin Cheesecakes.
Mini Cheesecakes are the perfect solution! A fun, easily served, Fall dessert recipe that anyone can make. If regular cheesecake makes you nervous, mini cheesecake is the perfect place to start.
And maybe you want a treat that’s a little healthier? These Skinny Mini Pumpkin Cheesecakes are gluten-free, dairy-free, and naturally sweetened with honey or maple syrup. They start with a crunchy pecan crust. Topped with a creamy, smooth, pumpkin cheesecake layer. And then, put a little cool whip on top! For the ultimate Holiday dessert.
Plus, there is NO flour used in these Mini Cheesecakes. Finding a good gluten-free flour can sometimes be a daunting task, especially if you’ve never bought any before. Forget about all that and make some Mini Pumpkin Cheesecakes, that everyone can still enjoy!
Let’s get to chatting about a few details to ensure mini cheesecake success.
Let’s start with the pecan crust on the bottom.
First, it’s a simple combination of finely chopped pecans, maple syrup (or honey), melted butter and water. You’ll stir all the ingredients together.
Next, you’ll take a muffin tin and line each cavity with cupcake liners. Spray them all lightly with non-stick spray. Then add an overflowing scoop of the pecan mixture to each cupcake liner. Use the back of your tablespoon to gently press the mixture to the bottom of each liner, in one even layer.
You’ll bake the crust in the oven prior to making the filling, so that you make sure you have a crunchy crust at the bottom.
The crust is a little sticky from the maple syrup, so it sticks together as a crust but isn’t entirely hard. It reminds me of Pecan Pie filling, which is incredible when combined with pumpkin cheesecake!
If you don’t have pecans (or don’t want to use them), you could also use finely chopped walnuts.
Then, the pumpkin cheesecake mixture.
You’ll beat your cream cheese first with a mixer till it’s smooth. Then, you’ll add the Greek yogurt, honey/maple syrup, pumpkin puree, pumpkin spice seasoning, and vanilla and mix them in entirely. Lastly, lightly mix your egg in.
Top your baked pecan crust with the mixture, filling each cupcake liner almost entirely full. Bake in the oven till you see just a slight jiggle in the center of your cheesecake.
After these Skinny Mini Pumpkin Cheesecakes cool, the middles cave in a bit. It’s normal for mini cheesecakes. And guess what, it’s the perfect spot for cool whip! 🙂
What makes this recipe “skinny” is using reduced fat cream cheese and Greek yogurt. Instead of using traditional cream cheese for all of it. If you want to meet in the middle, feel free to use regular cream cheese and not reduced fat, either one works.
I do not recommend using any other type of yogurt though. I prefer 2% plain Greek yogurt. You could use vanilla instead of plain, and then add only 1/2 teaspoon of extra vanilla extract into the filling instead.
If you don’t want to use honey or maple syrup, you could also use brown sugar in it’s place.
Don’t have pumpkin pie spice seasoning? You can mix together 2 teaspoons of cinnamon, and 1/4 teaspoon each of ginger, nutmeg, allspice, and cloves, to create your own!
Luscious cheesecake combined with pumpkin spice flavors, a crunchy and sweet Pecan Pie-like crust… you don’t wanna miss these Skinny Mini Pumpkin Cheesecakes! 🙂
And if you make these, let me know what you think! Either leave a comment below, or find me on Instagram. I love seeing what you guys make.
Looking for more easy, healthier, gluten-free, Holiday-inspired recipes? Check out my Chocolate Chip Pumpkin Bars or Pecan Pie Muffins.
And if you have leftover Greek yogurt, sweeten it with a little honey, add a little vanilla, and top it with some homemade granola!

- 1 cup pecans, finely chopped
- 3 tbsp maple syrup or honey
- 2 tsp water
- 1 tsp butter, melted
- 8 oz reduced fat cream cheese
- 1/2 cup Greek yogurt (I used 2%)
- 1/4 cup maple syrup or honey
- 1/2 cup pumpkin puree
- 1 1/2 tsp pumpkin spice seasoning
- 1 tsp vanilla
- 1 egg
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To prepare, preheat your oven to 325 and line a muffin tin with cupcake liners. I like to spray a little non-stick spray in mine too, just in case!
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In a small bowl, stir together your chopped pecans, honey, water and butter.
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Add an overflowing tablespoon of your pecan mixture to each cupcake liner, then use the back of your tablespoon measure to press the pecan mixture into the bottom of the liner in a flat, firm layer.
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Bake in the oven for about 13-14 minutes, or till the edges of the crust are starting to brown a touch and the crust feels a bit firm. *Create your pumpkin cheesecake filling while your crust is in the oven*
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In a large mixing bowl, beat your cream cheese with a hand mixer for a minute or two, till it's creamy and smooth.
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Add in your Greek yogurt, honey, pumpkin puree, pumpkin spice and vanilla, and blend again till smooth and everything is well incorporated.
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Add your egg into the mixture and blend briefly - only till the egg is well incorporated, do NOT over beat the mixture at this point!
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Once your mini pecan crusts are out of the oven, preheat your oven to 350. Fill each cupcake liner almost full (till just below the top of the liner). Repeat until all cupcake liners are filled with your pumpkin cheesecake filling.
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Bake in the oven for 17-20 minutes, or till the cheesecakes are set (with only a slight wiggle in the middle, when you jiggle your pan).
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Let your cheesecakes cool for 30 minutes on the counter. Then, put them in an airtight container and store them in your fridge.
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Serve with cool whip on top and extra pecans. Devour!
*These can be made ahead of time. Stored in an airtight container in the fridge they last about 5-6 days.
Could I use Swerve sweetener instead of honey or maple syrup? Happy holidays!
Hi there. I would not recommend trying to substitute with swerve.
If I want to make this as a standard-sized pie rather than individual mini ones, what would the bake time be?
Hi there. I wouldn’t recommend trying to make these as a standard sized pie. The amount of cheesecake would be less than you would need typically, so it wouldn’t turn out correct.
Are these made in mini muffin pan or regular size muffin pan?
Regular muffin pan.
Can you tell me a good swap for the pecans? My daughter can’t do Pecans but these sound so delicious and her 13th birthday is coming and I’d like to make these for her
Hi Jess. Any chance she could have walnuts instead? Those would also work great!
What adjustments would you make if making this in a larger pan, like an 8 by 8?
Thank you!
Hi Kristen. You could try making them in an 8×8 pan, and I would assume the cheesecake would just take longer to bake. Check these out, they’re sort of similar (although the crust is different) and they may help you direction-wise (you’ll just have to keep an eye on everything to make sure you don’t over bake the cheesecake layer): https://skinnyfitalicious.com/healthy-pumpkin-cheesecake-bars/
Can this recipe be made as traditional size muffins? Would there be any adjustmemts?
Hi Elizabeth. I’m sorry to say I’m not quite sure what you mean since they are already made inside a muffin tin? Do you mean without the cupcake liners?
Salted butter or unsalted ?
Either one will work! I typically use unsalted.
Any idea how to adjust this recipe in lower altitudes. I’m in Texas.
Hi Sara. These should work just fine in whatever altitude in Texas, this recipe is not specifically altered for high altitude!
I’m making these today for the 2nd time. They were outstanding!!!! Love the pecan crust !! Can’t wait to devour this batch L.o l…..
Awesome, Michelle! The crust is my favorite too!! Yum.
I haven’t put them in the oven yet but the cheesecake is soo runny. was that typical and it firms up?
Is the Greek yougurt plain or vanilla?
Hi Erin, I use plain Greek yogurt, but you can also use vanilla if that’s what you have on hand!
Can you tell me how many carbs are in each cupcake?
Hi Mona, about 239 calories each.