Keto Mini Cheesecake

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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!

Mini keto cheesecakes with almond flour and Besti.

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
Small keto cheesecake with berries on top.

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.
Keto mini cheesecake ingredients in bowls.
Have substitution questions?

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.

  1. Make crust. Mix almond flour, butter, Besti, and vanilla in a bowl.
  2. Press. Push the crust mixture into parchment lined muffin cups in a muffin tin. (This is a regular muffin tin, not a mini one!)
Mini keto cheesecake crust with almond flour and Besti, mixed in a bowl.
Small low carb cheesecake crusts pressed into a muffin tin.
  1. 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.

TIP: Keep the mixer on low to medium speed.

This helps avoid too many air bubbles in the filling.

Whipped cream cheese and Besti in a bowl.
Small keto cheesecake batter in a bowl.
  1. Fill. Add the cheesecake batter to the prepared muffin cups (you can fill them almost full).
  2. 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.

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.

Muffin tin filled with sugar-free mini cheesecake batter.
Baked keto mini cheesecake in a muffin tin.
  1. Chill. Let the keto mini cheesecake cool completely, then chill for 30 minutes, until set.
  2. Garnish. If desired, top the mini keto cheesecake recipe with fresh berries, such as raspberries, blueberries, or strawberries.
Low carb mini cheesecake on a cake stand.

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.
Mini keto cheesecake showing texture inside.

More Mini Keto Dessert Recipes

If you’re a fan of portion-controlled servings, try these other small sugar-free desserts:

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Tap on the times in the instructions below to start a kitchen timer while you cook.

  1. Preheat the oven to 350 degrees F (177 degrees C). Line a muffin tin with 12 parchment paper liners.

  2. 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.

  3. In a large bowl, use a hand mixer at low to medium-low speed to beat the cream cheese and powdered Besti, until fluffy.

  4. Beat in the egg, then the sour cream, lemon juice, and vanilla extract.

  5. Spoon the filling into the muffin cups. Smooth the top with a spatula.

  6. Bake for approximately 25 minutes, until the center is slightly jiggly. (Do not wait for it to fully set!)

  7. Cool cheesecakes in the pan on the counter to room temperature, then refrigerate for at least 4 hours (preferably overnight), until completely set.

Recipe Notes

Serving size: 1 mini cheesecake

Nutrition Facts

Amount per serving. Serving size in recipe notes above.

Calories 262

Fat 25g

Protein 6.3g

Total Carbs 5.7g

Net Carbs 3.7g

Fiber 2g

Sugar 1.8g

Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.

© Copyright Maya Krampf for Wholesome Yum. Please DO NOT SCREENSHOT OR COPY/PASTE recipes to social media or websites. We’d LOVE for you to share a link with photo instead. 🙂

Keto mini cheesecake recipe pin.

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