Keto Cheesecake Cupcakes

5 from 56 votes

These keto cheesecake cupcakes are so rich, smooth, and creamy, you won’t believe they are low carb! Made with simple ingredients, they take minutes to prep and perfect to serve as an elegant dessert. 3 grams net carbs per serving. 

keto cheesecake cupcakes

Keto Cheesecake Cupcakes

When it comes to keto cheesecakes, my favorite recipes to make are blueberry cheesecake, cheesecake bites, and these keto cheesecake cupcakes. 

It’s no secret that I love having my friends over for coffee or dessert. As the self appointed dessert king, my friends love coming over for something sweet, and lucky for them, I always change things up.

Recently, one of them requested a high tea for her birthday so instead of searching for one in our city, I opted to create one for her from scratch. As she follows a keto diet, I made mini versions of all my popular keto dessert recipes. I wanted to do something new, so instead of a full cheesecake, I made cheesecake cupcakes! 

I’ve been meaning to share a keto cheesecake cupcake recipe for quite some time. They make the perfectly portioned dessert when I’m craving something sweet and small! Now, these cheesecake cupcakes may look incredibly fancy but I promise you, they are so easy to make!

No sugar and no grains are needed, but you’d never tell. The texture of the filling is smooth and creamy and the base is dense and crunchy. The cupcakes are pleasantly sweet with a slight tang, without being overpowering. 

I had some friends over for the aforementioned high tea and served these cheesecake cupcakes and NO ONE believed me when I said that it was low carb- They thought it was full of sugar!

Ingredients to make keto cheesecake cupcakes

For the crust

  • Shortbread cookies– Any crushed up keto cookie can be used but I prefer using shortbread, as they remind me so much of graham crackers.
  • Butter– Melted and unsalted butter. Dairy free butter can also be used.

For the filling

  • Cream cheese– Softened to room temperature. 
  • Granulated sweetener of choice– I used erythritol, but monk fruit sweetener and allulose can both be used.
  • Sour cream– Balances the creaminess of the filling, while adding an extra tang.
  • Eggs– Room temperature eggs. 
  • Lemon juice– Just a pinch to balance out the other ingredients and give a lovely and light citrus note. 

How do you make low carb cheesecake cupcakes?

Start by greasing 18-20 muffin liners and divide them amongst two 12-count muffins. Next, combine your crushed cookies with melted butter until combined. Distribute the cheesecake base amongst the muffin liners and press down to fill the base. Bake at 180C/350F for 10 minutes, until golden and cooked. Remove the crusts from the oven and reduce the heat to 150C/300F.

Now, add your cream cheese into a large mixing bowl and beat together, until smooth and creamy. Add the remaining ingredients and beat together until smooth. Divide the mixture amongst the muffin liners and place back in the oven for 22-25 minutes, until it has set. 

Finally, remove the cheesecake cupcakes from the oven and let them cool completely. Once cool, refrigerate for at least 4 hours to firm up. 

low carb cheesecake cupcakes

Tips to make the best cheesecake cupcakes

  • You must reduce the heat after the crust has been baked, otherwise, the cheesecake filling will overcook around the edges but fall apart once they cool down.
  • Any cookie can be used for the crust. I prefer using a mild tasting one, hence the shortbread. 
  • Cool your cheesecake cupcakes to room temperature, before transferring them to the refrigerator. 
  • Top your cupcakes with whipped cream or low carb berries.

Storing and freezing cheesecake cupcakes

  • To store: Cheesecake cupcakes must always be stored in the refrigerator, covered, for up to 2 weeks. 
  • To freeze: Place leftover cheesecake cupcakes in a ziplock bag and store them in the freezer for up to 6 months. 

cheesecake cupcakes

More keto cheesecake recipes to try

keto cheesecake cupcakes

Keto Cheesecake Cupcakes

These keto cheesecake cupcakes are so smooth, rich, and creamy, you won't believe they are low carb! Simple ingredients and minimal prep needed, they make a fabulous dessert!
5 from 56 votes
Print Rate
Course: Dessert
Cuisine: American
Prep Time: 5 minutes
Cook Time: 25 minutes
Total Time: 30 minutes
Servings: 18 servings
Calories: 150kcal
Author: Arman


For the crust

For the filling


  • Preheat the oven to 180C/350F. Grease 2 12-count muffin tins and fill 18 of them with muffin liners.
  • In a mixing bowl, mix the crust ingredients until combined. Distribute them amongst the muffin liners and press them into the bottom. Bake for 10 minutes, until firm. Remove the muffin pans from the oven.
  • Reduce the heat to 150C/300F. In a mixing bowl, beat the cream cheese until smooth. Add the remaining ingredients and beat until combined and smooth.
  • Divide the mixture amongst the muffin cups, until full. Bake for 22-25 minutes, or until set.
  • Remove from the oven and let cool completely, before refrigerating for at least 4 hours.


TO STORE: Cheesecake cupcakes must always be stored in the refrigerator, covered, for up to 2 weeks. 
TO FREEZE: Place leftover cheesecake cupcakes in a ziplock bag and store them in the freezer for up to 6 months.


Serving: 1serving | Calories: 150kcal | Carbohydrates: 6g | Protein: 4g | Fat: 14g | Sodium: 122mg | Potassium: 62mg | Fiber: 4g | Vitamin A: 527IU | Vitamin C: 1mg | Calcium: 43mg | Iron: 1mg | NET CARBS: 2g
Tried this recipe?Give us a shout at @thebigmansworld or tag #thebigmansworld!

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    6 thoughts on “Keto Cheesecake Cupcakes

    1. 5 stars
      These were fun and easy to make! I used the shortbread cookies and they tasted amazing!!! I will be having these as a regular summer dessert! Keto is so east when you get to enjoy a dessert like this!! Thank you!!!

    2. 5 stars
      I am following a strict low carb diet; so instead of using cookies, I substituted walnuts; crushed one cup with 2 T butter, pressed it into cupcake liners. I also reduced the ingredients to make 12 not 18.

    3. 5 stars
      So tasty 😋- My T1D son absolutely loved them. These cakes will be on high rotation. Thank you so much for sharing the recipe.

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