Skip to content

Chocolate Peanut Butter Mini Keto Cheesecakes in a Muffin Tin

Easy mini keto cheesecakes in a muffin tin! – These simple low carb cheesecakes are decadent and delicious. Creamy, smooth, sugar free cheesecake filling, a swirled dark chocolate and peanut butter topping, with a buttery pecan crust. Ready in well under an hour!

Chocolate peanut butter muffin tin keto cheesecakes on a wooden board.

Each mini chocolate peanut butter cheesecake has under 4g net carbs! A perfect low carb treat for satisfying that sweet craving. 




Two bite keto cheesecakes are an easy low carb dessert that anyone can make. Using only common low carb ingredients, and a standard muffin, mini cheesecakes are baked in just 20 minutes and on the table in under an hour. A simple keto friendly cheesecake that can be made with or without a water bath.

Why You'll Love Mini Keto Cheesecakes

  • Mini cheesecakes are a perfect low carb snack to satisfy that sweet tooth when you don’t want a full cheesecake in the house.
  • Rich dark chocolate + creamy peanut butter…need I say more?
  • This dessert is easy to make and uses common low carb baking ingredients.
  • Low in sugar and net carbs perfect for keto and other low sugar diets. 
  • Mini cheesecakes are great for sharing as a party snack or low carb holiday dessert.
  • Easy to make in a standard muffin tin, no special cheesecake pan required. Made with or without a water bath. 
Mini muffin tin keto cheesecakes stacked on a wooden board with a bite out of them showing the chocolate and peanut butter inside.

Tips for mini keto cheesecakes

  • Bring the ingredients to room temperature. Let the cream cheese, sour cream, and eggs sit on the counter until they come to room temperature before you start preparing the cheese cake. 
    • The cream cheese needs to soften so it mixes into a smooth batter. If the eggs and sour cream are cold when you add them to the cream cheese it can cause the cheese to re-harden leading to a lumpy cheesecake batter.
    • Place cold eggs in warm water for 5-10 minutes to bring them to room temperature quickly. 
  • Test the texture of the crust and adjust as needed. After mixing the butter with the crust, grab a handful of the mixture and squeeze firmly in your hand. The texture should hold its shape and not crumble apart or ooze butter. It should be like damp sand. If it’s too crumbly add more melted butter, if it’s too buttery add more pecans.
  • Pre-bake the crust. Although technically you can get away without prebaking the crust, doing so gives you a crispier, sturdier cheesecake crust with better flavour. 
  • Avoid over baking. Cheesecake will continue baking after you turn off the oven. The trick is to stop baking once the outsides appear firm but the center is still slightly jiggly. It should not be soupy, just a slight jiggle jiggle. 
    • For a more precise indicator, check the internal temperature of the cheesecake with a candy thermometer. It should be 150°F [66°C]
  • Cool slowly in a warm oven. Once the baking is finished, crack open the oven door and turn off the oven, let the mini cheesecakes cool for 10-15 minutes in the warm oven. Allowing the cheesecake to slowly cool will prevent cracking and sinking. If you need the oven for something else, place the cheesecake on the stove top which should be slightly warm from the oven. 
    • Tip: Use a wooden spoon to keep the oven door cracked open. 
  • Use a water bath for perfect mini cheesecakes. You don’t need a water bath for this recipe. But using one makes the cheesecakes creamier and smoother, and will prevent sinking and cracking. The top will be perfectly flat and smooth. It’s much easier to use a water bath for mini cheesecakes since a muffin tin is sealed from the bottom so there is no chance of water leaking in, making the crust soggy. 
  • Cool fully before refrigeration. Make sure the cheesecakes fully cool to room temperature before storing in the fridge or freezer. Cooling too quickly can shrink, sink, and crack the cheesecakes.
Mini chocolate peanut butter keto cheesecake sliced in half drizzled with chocolate.

Should You Use a Water Bath for Mini Cheesecakes?

A water bath (Aka and Bain-Marie) can be kind of a pain when making a cheesecake. Not only do you need a big oven safe pan for the water to go in, you usually have to seal up the springform pan with tin foil to prevent leaking. Luckily, with mini keto cheesecakes you don’t have that problem. The muffin tin used is already sealed so there is no chance of leaking. But do you even need to use a water bath?

A comparison photo of two mini keto cheesecakes no water bath on the left and waterbath on the right.

Water Bath vs. No Water Bath Cheesecake Comparison

Take a look at the image above and you can see there are noticeable differences between the two cheesecakes. The cheesecake cooked in a water bath has a perfectly uniform flat top and the filling is noticeably creamier and softer. The cheesecake is delicate, decadent and rich. 

The cheesecake cooked without a water bath has sunk in the middle and the filling is somewhat more firm and cakey, although still incredibly rich, soft, and delicious, 

Neither of these is right or wrong, it depends what you are looking for.

If you want an easy quick recipe with less fuss. Skip the water bath, and use the sunken top as a bowl for extra fillings. 

If you want a perfectly flat uniform cheesecake with a slightly creamier filling, use the water bath.

Mini Keto Cheesecake Variations

Cheesecake is incredibly versatile and these mini low carb cheesecakes are no exception. Different flavours can be added to the crust, the cheesecake mixture or the toppings. 

Crust Variations – In place of crushed pecans you can use any low carb nut you prefer. Almond flour, cashews, walnuts, etc. Do not use coconut flour, it will not work. Try adding some warm spices to the crust to add flavour. Cinnamon, pumpkin spice, nutmeg, star anise, cardamom, or cloves work well in a cheesecake crust. 

Topping Variations – Instead of peanut butter and chocolate, any of your favourite low carb toppings or fruit can be added to these mini keto cheesecakes. Strawberries, raspberries, blueberries, pecans, keto caramel, low carb jam.

A variety of mini low carb cheesecakes on a white marble surface.
Maple Pecan, Cran-raspberry, and chocolate peanut butter keto cheesecakes.

More keto cheesecake recipes you’ll love

Mini Muffin Tin Keto Cheesecake FAQs

Can you freeze mini cheesecakes?

Keto cheesecakes are a great make ahead dessert to keep on hand for when you need them. Wrap the cooked cheesecakes in plastic wrap and place in an airtight container. Freeze for 1-2 months. Thaw in the fridge overnight or on the counter at room temperature. 

Do You need a special cheesecake pan for mini cheesecakes?

These easy mini cheesecakes are made in a standard muffin tin, no need for a special cheesecake pan. If you have a mini cheesecake pan feel free to use it. 

Can this recipe make a full cheesecake?

This recipe uses the exact same formula as a full size cheesecake, you could easily use this recipe to make a full size cheesecake if you wish. You may need to increase the amount of crust mixture you make. 

How do you know when cheesecake is done?

Pay attention to the center of the cheesecake, it should just slightly jiggle when you tap the pan. You don’t want it to be runny, but you don’t want it to be fully set either. It will finish firming up as it cools. 

To be sure you can use a candy or meat thermometer and turn off the heat when the internal temperature is 150°F [66°C]

Do these cheesecakes need a water bath?

A water bath is optional for mini keto cheesecakes which is why they are so easy to make. However, using a water bath will make the cheesecakes completely uniform and the texture will be smoother and creamier. See the tips sections above for more details about using a water bath.

Why do cheesecakes sink in the middle?

Cheesecakes sink in the middle due to uneven heating and cooling. Although this does not affect the flavour it can change the texture. Using a water bath and cooling the cheesecakes slowly can prevent sinking. If you are fine with a little sinking then use that divot to keep the toppings in place.

Why does cheesecake crack?

Similar to sinking, cheesecakes crack from uneven heating and cooling. These minis tend not to crack but cooling them too quickly is still not recommended. Cool them slowly in a warm oven but turning off the oven and cracking the door slightly while they cool.

Is cheesecake keto friendly?

A normal cheesecake is not keto friendly with its high carb graham cracker crust and copious amounts of sugar. But this easy recipe is completely keto friendly thanks to the low carb pecan crust and monk fruit/erythritol sweetener used. 

What crust is used for keto cheesecake?

Instead of graham crackers this recipe uses crushed pecans. Pecans are full of healthy fats and are one of the lowest carb nuts available. 

Can I substitute almonds/almond flour for the pecans?

Any nut of choice can be used in place of pecans. Almond flour or any ground nuts make an excellent crust for a low carb low sugar cheesecake. 

Best keto friendly sugar substitute for keto cheesecake?

Choose the low carb sweetener you prefer and are familiar with. Allulose, erythritol, and monk fruit are all great choices.

Should I use powdered sweetener for low carb baking?

Yes, always. Unlike sugar, low carb sweeteners do not dissolve nicely into baked goods making them appear less sweet. Using powdered sweetener evenly distributes the sweetness and gives keto baked goods a pleasantly sweet flavour.

How Do I Get Powdered Keto Friendly Sweetener?

Powdered erythritol can be purchased online or you can easily powder your own using a coffee grinder.

Muffin tin chocolate peanut butter keto cheesecakes being unwrapped from muffin papers.

Recipe Card

Low Carb Chocolate Peanut Butter Mini Cheesecakes

Mini chocolate peanut butter keto cheesecake on a wooden board.
Prep Time 20 minutes
Cook Time 20 minutes
Cooling Time 20 minutes
Servings 18 cheesecakes
Calories 273 kcal
Net Carbs 3.9 g
Rate this Recipe
These mini two bite cheesecakes are made in a muffin tin and are ready in under 60 minutes. An easy keto friendly dessert topped with creamy peanut butter and rich dark chocolate, perfect for entertaining, holidays, or satisfying that sweet tooth.

IMPORTANT – There are often Frequently Asked Questions within the blog post that you may find helpful. Simply scroll back up to read them!



  • 3x 6 cup muffin tin
  • Large Mixing Bowl
  • stand mixer or electric mixer
  • 18 standard baking cups paper or silicone


Low Carb Cheesecake Crust

  • 2 cups pecans coarsely ground
  • 2 tablespoons powdered sweetener erythritol, monk fruit, or allulose
  • ¼ cup butter melted
  • ¼ teaspoon salt

Low Carb Cheesecake Mixture

  • 16 oz cream cheese room temperature
  • cup sour cream
  • ½ cup powdered sweetener erythritol, monk fruit, allulose
  • 2 large eggs room temperature
  • teaspoons vanilla extract



  • Preheat the oven to 325℉ [165℃].
  • Prepare cheesecake crust. Add the pecans to a food processor and grind into crumbs. Add the ground pecans to a large bowl and add the powdered sweetener, melted butter, and salt. Combine well until the mixture is thick and coarse like wet sand. It should hold together when lightly squeezed but should not ooze butter.
    2 cups pecans, 2 tablespoons powdered sweetener, ¼ cup butter, ¼ teaspoon salt
    Keto pecan cheesecake crust being squeezed the right texture.
  • Beat cream cheese until smooth. In the bowl of a stand mixer or an electric hand mixer beat the softened cream cheese and powdered sweetener on high for 2-3 minutes until light and fluffy. Add the sour cream and vanilla extract, beat until combined.
    16 oz cream cheese, ⅓ cup sour cream, 1½ teaspoons vanilla extract, ½ cup powdered sweetener
  • Beat in the eggs. With the mixer running at medium speed, add the room temperature eggs one at a time, make sure each egg is fully incorporated before adding the next.
    2 large eggs
    Keto cheesecake mixture in the bowl of a stand mixer.
  • Prebake the crusts. Line the muffin tins with baking cups and add 2-3 tablespoons of crust mixture to each one. Use a small measuring cup or shot glass to lightly press the crust mixture evenly into the bottom of each baking cup. Bake at 325℉ [165℃] for 12-15 minutes. Remove the pan from the oven and set on a baking rack until the crusts are cool.
    Keto pecan cheesecake crust being pressed into a muffin paper lined baking pan.
  • Fill the cheesecakes. Once the crusts have cooled, fill each of the baking cups with approximately ¼ cup of filling, they should be about ¼ inch [6 mm] from the top.
    Unbaked keto mini cheesecakes in a muffin tin.
  • Add the topping. Melt the peanut butter and dark chocolate separately in to two microwave safe bowls. Heat at 30 second intervals until soft and melted. Use a spoon to drizzle about 1 tablespoon of each over the top of the unbaked cheesecakes. Using a knife or toothpick, swirl the peanut butter and chocolate into the top layer of each cheesecake.
    ½ cup Lily's dark chocolate, ½ cup peanut butter
    Chocolate and peanut butter swirled into the top of unbaked mini cheesecakes.
  • Bake cheesecakes. If using the optional water bath pour 2 inches [5 cm] of hot water in a large roasting pan. Place the muffin tin in the roasting pan with the hot water. Bake in the center of a 325℉ [165℃] oven for 20 minutes until the edges are firm and the center still has a slight jiggle to it.
  • Cool cheesecakes slowly. Turn off the oven and leave the door of the oven cracked with a wooden spoon to let heat escape. Let the cheesecakes cool in the oven for 10-15 minutes before removing. Allow the cheesecakes to cool completely before attempting to remove them from the baking cups.
    baked chocolate peanut butter keto cheesecakes on a wood board being unwrapped


Crust Variations: In place of ground pecans, ground almonds, almond flour, or your preferred ground nut can be used. 
Silicone Baking cups make removal clean and easy!
You Know They Are Done When: The cheesecakes are finished baking when the edges are fully set and the middle just slightly jiggles when you gently shake the muffin tin. You can also check the internal temperature with a thermometer to make sure its at least 150℉ [66℃]
Swirling the topping into the top of the cheesecakes is optional but gives them a nice appearance and adds flavour throughout each bite. 
Waterbath vs. No Waterbath: Water bath is optional but does lead to a very creamy and uniform cheesecake. For more information about the differences between a waterbath and no waterbath, read this dedicated section. 
Low Carb Dark Chocolate: Lilys low carb Dark chocolate bars are stevia and erythritol sweetened white chocolate that is very low in net carbs. If you can't find Lilys use any of your preferred low sugar dark chocolate such as Lindt excellence 85% dark chocolate or Lakanto Chocolate baking Chips. You can also simply omit it from the recipe. 


Calories: 273kcalCarbohydrates: 11.2gProtein: 5.7gFat: 25gSaturated Fat: 10gSodium: 130mgPotassium: 96mgFiber: 2.8gSugar: 2.3gCalcium: 41mgSugar Alcohols: 4.52gNet Carbs: 3.9g

Nutritional information is calculated using the recipe calculator and verified database available from Cronometer. Although every reasonable effort is made to provide accurate information this estimate is provided as courteously and convenience only. To obtain the most accurate representation of the nutritional information in any given recipe, you should calculate the nutritional information with the actual ingredients used in your recipe.

Try the free recipe calculator at Cronometer
Did you give this a try?Mention @yummyforadam or use #yummyforadam on instagram!
Looking for a different low carb recipe?Something you don't see here or looking for a low carb version of your favourite recipe? Let me know so I can get working on it! Contact me directly or leave a comment!
Keywords: christmas dinner, easter dessert, easy keto dessert, keto dessert, low carb dessert, low carb holiday desserts, low carb holiday recipes, mini keto cheesecakes, Thanksgiving sides




Mini muffin tin keto cheesecakes on a wooden board surrounded by low carb chocolate chips and peanut butter.


Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating