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Whether you’re looking for easier portion control or just prefer your keto desserts fun-sized, this keto mini cheesecake recipe is the perfect little treat! It has everything you love in the full sized version (based on the popular large keto cheesecake!)… but made a little smaller for easier handling. These small keto cheesecakes still have the same buttery crust and creamy filling, all in a handheld package. Since they are made in a regular muffin tin (not a mini one) and do have a crust, they are larger and more filling than my crustless cheesecake fat bombs, which are more of a bite-sized treat.
For the best mini keto cheesecake, ingredients matter! A combination of finely milled Wholesome Yum Almond Flour and Besti creates the perfect sweet, buttery shortbread crust, with no gritty texture, aftertaste, cooling effect, or crystallization that other flours and sweeteners sometimes have. Meanwhile, Besti Powdered ensures that the filling is silky smooth, because it dissolves easily and completely. Plus, both versions of Besti have 0 net carbs, but taste just like sugar!

Why You’ll Love This Keto Mini Cheesecake Recipe
- Buttery shortbread crust
- Smooth, creamy filling
- Easier (and less prone to cracking) than a larger cake
- Just 40 minutes from start to finish — faster than a larger cake
- Only 3.3 grams net carbs each
- Great for portion control

Ingredients You’ll Need
This section explains how to choose the best ingredients for keto mini cheesecakes, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.
This mini cheesecake keto recipe uses similar ingredients you’d expect in a full-sized keto cheesecake.
For The Crust:
- Wholesome Yum Almond Flour – It’s finely milled for the best texture! Never worry about gritty crust again.
- Butter – Helps hold the crust together and adds buttery flavor. Make sure it’s softened.
- Besti Monk Fruit Allulose Blend – Using the granulated version creates better crust texture, but if you want to just get one type, get the powdered which can work for both crust and filling.
- Vanilla Extract
For The Filling:
- Cream Cheese – Essential for a small keto cheesecake! Use a full-fat cream cheese and soften at room temperature, so it blends silky smooth.
- Besti Powdered Monk Fruit Allulose Blend – Using the granular version creates better crust texture, while the powdered version helps the filling stay silky smooth.
- Egg – Use whole, large eggs. These hold the filling together and make it thick. Make sure the egg is at room temperature, so it doesn’t solidify the cream cheese.
- Sour Cream – Softens the texture of the cream cheese. Use a full-fat version, and make sure it’s room temperature.
- Lemon Juice – Balances and brightens up the heaviness from the cream cheese.
Have substitution questions?
I go over substitutions in detail in my main keto cheesecake recipe post. Check there first!

How To Make Keto Mini Cheesecake
This section shows how to make small keto cheesecake, with step-by-step photos and details about the technique. For full instructions, see the recipe card below.
- Make crust. Mix almond flour, butter, Besti, and vanilla in a bowl.
- Press. Push the crust mixture into parchment lined muffin cups in a muffin tin. (This is a regular muffin tin, not a mini one!)


- Make filling. Beat cream cheese and powdered Besti until fluffy. Add the egg, followed by sour cream, lemon juice, and vanilla extract.

TIP: Keep the mixer on low to medium speed.
This helps avoid too many air bubbles in the filling.


- Fill. Add the cheesecake batter to the prepared muffin cups (you can fill them almost full).
- Bake. Bake keto-friendly mini cheesecakes until center is just slightly jiggly in the center. (Do not wait for them to fully set!)

TIP: The cheesecakes are done when the center is slightly jiggly, like an almost-set jello.
Do not wait for them to be fully set in the oven, or they will be dry and crack when they cool. They will fully set after cooling and chilling.


- Chill. Let the keto mini cheesecake cool completely, then chill for 30 minutes, until set.
- Garnish. If desired, top the mini keto cheesecake recipe with fresh berries, such as raspberries, blueberries, or strawberries.

Small Keto Cheesecake FAQs
Below are answers to the most common questions about this recipe, but you may also want to check out my main keto cheesecake post for more tips and questions answered.
Is Mini Cheesecake Keto?
Most mini cheesecake recipes are not keto, since many of them use white flour and sugar that can bump up the carb count. With a few changes to the flour and sweetener, we made this mini cheesecake recipe keto!
Why Did My Mini Cheesecakes Sink?
A keto cheesecake mini recipe can sink for several reasons:
- Under-baking. The bottom needs to be fully cooked to support the top, and not baking for long enough can lead to sinking.
- Over-baking. Baking the mini low carb cheesecakes for too long can cause them to sink, crack, or both.
- Over-mixing. Beating too long or at too high speed can create too many bubbles in the batter, which can cause rapid rising followed by sinking.
How To Remove Mini Cheesecakes From The Pan?
There are a few ways to remove low carb mini cheesecake without damaging it:
- Invert. You can allow the pan to cool completely on a wire rack, then invert to remove.
- Tweezers. This is the method we usually use. Just grab the edge of the muffin liner with tweezers and carefully lift.
- Extra parchment. Before lining the pan, cut long strips of parchment and add them to the muffin pan (one underneath each paper cup, with ends exposed). This can create a set of “handles” for each keto mini cheesecake, so you can remove them easily.
Storage Instructions
- Store: Like any cheesecake, keto mini cheesecakes keep very well. Store them in the fridge for up to 5 days.
- Freeze: Place the cakes on a sheet pan and freeze until solid, then wrap tightly in foil or plastic wrap and transfer to a freezer bag. Freeze for 6-8 months.
- Thaw: Before serving, remove the wrapping and thaw in the refrigerator, or on the counter.

More Mini Keto Dessert Recipes
If you’re a fan of portion-controlled servings, try these other small sugar-free desserts:
Tools To Make Small Keto Cheesecake
- Hand Mixer – For making the filling.
- Muffin Tin – The perfect size for this mini keto cheesecake recipe.
- Cupcake Liners – These are made from parchment paper, so work better than regular paper ones.
Keto Mini Cheesecake Recipe
Reader Favorite Recipes
The recipe card is below! Readers that made this also viewed these recipes:
Keto Mini Cheesecake (Like The Real Thing!)
This easy low carb keto mini cheesecake recipe has a buttery crust, creamy filling, and just 3g net carbs! Learn how to make small keto cheesecakes perfectly every time.
Recipe Video
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Ingredients
Tap underlined ingredients to see where to get them. Please turn Safari reader mode OFF to view ingredients.
Cheesecake Crust:
Filling:

Get Keto Sweetener For This Recipe
GET BESTIInstructions
Tap on the times in the instructions below to start a kitchen timer while you cook.
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Preheat the oven to 350 degrees F (177 degrees C). Line a muffin tin with 12 parchment paper liners.
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In a medium bowl, stir together the almond flour, melted butter, Besti, and vanilla extract, until uniform. The dough will be slightly crumbly. Press the dough into the bottom of the muffin cups.
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In a large bowl, use a hand mixer at low to medium-low speed to beat the cream cheese and powdered Besti, until fluffy.
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Beat in the egg, then the sour cream, lemon juice, and vanilla extract.
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Spoon the filling into the muffin cups. Smooth the top with a spatula.
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Bake for approximately 25 minutes, until the center is slightly jiggly. (Do not wait for it to fully set!)
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Cool cheesecakes in the pan on the counter to room temperature, then refrigerate for at least 4 hours (preferably overnight), until completely set.
Last Step: Leave A Rating!
Share your recipe picture by tagging @wholesomeyum and hashtag it #wholesomeyum on Instagram, or in our Facebook support group, too – I’d love to see it!
Recipe Notes
Serving size: 1 mini cheesecake
Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.
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48 Comments
Lorri Miller
I haven’t tried this yet. But wondering if these can be stored in the freezer or if that would affect the texture? Thanks
Wholesome Yum D
Hi Lorri, Place the cakes on a sheet pan and freeze until solid, then wrap tightly in foil or plastic wrap and transfer to a freezer bag. Freeze for 6-8 months.
Valentina
These keto mini cheesecakes are truly amazing! The flavors are so delicious and the fact that they are healthier than the classic ones is a YES!
April
You can’t even tell these are Keto! That crust is FANTASTIC, the filling is rich and creamy – wonderfully delicious!
Erin
I like the way the butter crust pairs perfectly with the cheesecake filling. It was an easy recipe to follow.
Erica
Would I need to make any changes to the baking time if I omitted the crust? The crust sounds delicious but when it comes to cheesecake, it’s all about the filling for me 🙂
Maya | Wholesome Yum
Hi Erica, Probably not, but you can check on them a few minutes early just in case.
Susan B
This looks delicious! Can’t wait to try it. I don’t see the video, however, anywhere in this post. Can you help?
Maya | Wholesome Yum
Hi Susan, The video is right above the ingredients on the recipe card.
Tavany
How do I prevent them from caving in.
Maya | Wholesome Yum
Hi Tavany, I covered this in the FAQs section above.
Eileen
OMG these are delicious! Tastes like the real thing. I used silicone cupcake liners and they came out perfect, no time adjustments, and they popped right out.
Eileen
Can I make this recipe with a silicone muffin pan instead of using cupcake papers?
Maya | Wholesome Yum
Hi Eileen, Yes, you can do that!
Kathy
This sounds great! I was wondering about making these truly mini by making them in a 24 count mini muffin pan. A lot more work but I have a banquet to go to. I was thinking of cutting baking time in half and checking every couple of minutes after that. Everything else the same?
Maya | Wholesome Yum
Hi Kathy, Yes, it should work in a mini muffin tin and half the baking time is a good starting point.
Annie
Can I use Besti Allulose instead of the Monkfruit?
Maya | Wholesome Yum
Hi Annie, Yes, you can! You’ll need to use about 30% more sweetener.
Angela Schwab
Do you have a nut free mini cheesecake recipe?
Maya | Wholesome Yum
Hi Angela, You can use the coconut flour crust from these cheesecake cupcakes.
Joyce Thedford
I do not have any Besti Monk Fruit Allulose Blend. Is there something else I can use in it’s place. I really want to try these.
Maya | Wholesome Yum
Hi Joyce, This recipe has only been tested with Besti and I can only guarantee results with that. You can get Besti here for the crust and get Besti Powdered here for the filling.
Carolynne Timko
These look delicious and exactly what I need for a party on Wednesday – can I use (other sweetener brand) instead of Monk fruit? I just ran out of monk fruit but have plenty of (other sweetener brand). Thanks – I am using more and more of your recipes and have been getting a lot of praise for what I make. I am also going to try your pumpkin roll and wonder the same – can I use (other sweetener brand)? Thanks
Maya | Wholesome Yum
Hi Carolynne, This recipe has only been tested with Besti and I can only guarantee results with that. Other sweeteners tend to crystallize and get gritty, which was one of the reasons I created Besti. 🙂 If you need to stock up, you can get Besti here for the crust and get Besti Powdered here for the filling.
Nadya
I’ve made these several times, very easy to do, just literally toss everything together and blend. I’ve even put them in miniature cups and when u put a piece of fruit on it and a little whip cream, omg so good and it hits the spot, wonderful recipe.
prncsdi
MAKE THESE!!! 10 stars all the way!
We are lovers of desserts & have been trying to find recipes that don’t use sugar but are still delicious.
We invited friends over for dinner and I made these, served them with fresh blueberries and fresh sliced strawberries. The store was out of sugar free whipped cream but it didn’t matter. These were super delicious and I’m making them again just for us.
** these did NOT have the aftertaste that so many keto desserts do**
Thank you so much for sharing!
Mark Dossett
Very easy and tasty recipe
MLee
Are these mini cheesecakes made in MINI muffin-size tins or regular muffin size tin?
Maya | Wholesome Yum
It’s a regular sized muffin tin.
Glenna
We are brand new to keto type of cooking and since my son loves cheesecake, your mini cheesecake recipe is fantastic. Thank you for your recipes
Cathe Bedard
These sound so delicious! Please try to recreate them with no gluten and no dairy.
thanks!
Maya | Wholesome Yum
Hi Cathe, They are already gluten free. We don’t currently have a dairy free version but will add it to our list for the future.
Darlene Geisler
Does anybody have recipes using the bread mix?
Maya | Wholesome Yum
Hi Darlene, I do have recipes with the bread mix and more coming soon. Here are a few: keto French toast (swap the bread instructions with slices of the bread made from bread mix), keto yeast bread, low carb peanut butter and jelly, and keto croutons.
Katie
Can’t even tell they’re keto. We love these!
Richelle
This is by far the best keto cheesecake that i tried! I made these and the whole family loved it including my picky husband, lol! I also tried your NY style cheesecake recipe which is also delicious but for me, this is by far the winner.
Natalie
These mini desserts are the best!! Super sweet & creamy, they are the perfect little dessert!!
Beth
Oh my goodness! These mini cheesecakes are such a huge hit! My husband and daughter love this!
Kate
I can’t believe these are Keto – they are so incredibly decadent and delicious, you’re so clever!
Amy L Huntley
I am always looking for desserts that my daughter with celiacs can eat. This recipe is a keeper for sure. You couldn’t even tell that it was Keto. So yummy! We added some fresh fruit on the top too!
Beth Sachs
Love these bitesize cheesecakes. So creamy and delicious! They are great for picnics!
Kylie
I’m taking these to a party this week! They are so good!
Roxie
When do add the sour cream?
Maya | Wholesome Yum
Hi Roxie, Sorry about that! Beat in the sour cream right after the egg.
Carolyn
Thank you so much! I’m assuming you put the sour cream in when beating the cream cheese?
Maya | Wholesome Yum
Hi Carolyn, Sorry, we updated the recipe card. Beat in the sour cream right after the egg.
RL S
I don’t see where to add the sour cream – assuming after beating the egg and cream cheese? or with them?
Also wondering how this would work in the microwave, since heating the kitchen in the summer is not optimum!
Maya | Wholesome Yum
Sorry, the recipe card is updated now — beat in the sour cream right after the egg. I haven’t tried these in the microwave, but think they might be prone to overcooking. Let us know how it goes if you try it!