Cheesecake Cupcakes


5 from 121 votes
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These cheesecake cupcakes are so rich, smooth, and creamy, you won’t believe how easy they are to make! Using simple ingredients, they need just two minutes of prep time. 

cheesecake cupcakes.

When it comes to keto cheesecakes, my favorite recipes to make are a Biscoff cheesecake, caramel pecan cheesecake, and these keto cheesecake cupcakes. 

If you’ve tried our cheesecake bites, you’ll love this baked version of them! 

Why this recipe works

  • Two minutes prep. All you do is prep the crust and the filling and that is it. 
  • 7 simple ingredients. Basic cheesecake ingredients like cream cheese and eggs. 
  • Naturally gluten-free. When made using gluten-free cookies, these are suitable for celiacs. 

What I love about this recipe is how incredible it tastes. 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. 

Ingredients needed

This recipe calls for simple and pantry staple ingredients. If you’ve made any of my cheesecake recipes before, you’ll likely have everything on hand. Here is what you’ll need: 

For the crust

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

For the filling

  • Cream cheese. Softened to room temperature. 
  • Sugar. White sugar or raw sugar. 
  • 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 to make cheesecake cupcakes

This recipe requires less than five minutes of hands-on/prep time, so really, the oven takes care of all the hard work. Ready to make some cheesecake cupcakes? 

Step 1- Make the crust and par-bake it

Start by greasing 18-20 muffin liners and divide them among 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.

cheesecake crust.

Step 2- Make the cheesecake mixture

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.

cheesecake filling.

Divide the mixture among the muffin liners and place back in the oven for 22-25 minutes, until it has set. 

pre-baked cheesecake cupcakes.

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

cheesecake cupcake.

Tips to make the best recipe

  • 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. You can also use a store-bought crust, like I often use in my lemon or cherry cheesecake.
  • Cool your cheesecake cupcakes to room temperature, before transferring them to the refrigerator. 
  • Feel free to top your cupcakes with fresh berries, whipped cream, or some melted chocolate

Storage instructions

  • 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 cupcake recipe.

More cheesecake recipes to try

Frequently asked questions

How do you tell if cheesecake cupcakes are done?

Like a standard baked cheesecake, once the filling springs back lightly when touched, the cupcakes are done.

How do you keep cheesecake cupcakes from falling down?

Carefully grease the muffin tins and/or line the muffin tin with muffin liners to give the cupcakes extra sturdiness.

What is the secret to a good cheesecake?

Using a combination of cream cheese and sour cream guarantees a perfectly creamy and rich filling every time.

cheesecake cupcakes recipe.

Cheesecake Cupcakes

5 from 121 votes
These cheesecake cupcakes are so rich, smooth, and creamy, you won't believe how easy they are to make! Using simple ingredients, they need just two minutes prep time. 
Servings: 18 cheesecake cupcakes
Prep: 5 minutes
Cook: 25 minutes
Total: 30 minutes


For the crust

For the filling

  • 2 cups cream cheese softened
  • 1 cup sugar
  • 1 cup sour cream
  • 2 large eggs
  • 1 teaspoon lemon juice


  • 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: 1servingCalories: 150kcalCarbohydrates: 6gProtein: 4gFat: 14gSodium: 122mgPotassium: 62mgFiber: 4gVitamin A: 527IUVitamin C: 1mgCalcium: 43mgIron: 1mgNET CARBS: 2g
Course: Dessert
Cuisine: American
Author: Arman Liew
Tried this recipe?Give us a shout at @thebigmansworld or tag #thebigmansworld!

Arman Liew

I’m a two time cookbook author, photographer, and writer, and passionate about creating easy and healthier recipes. I believe you don’t need to be experienced in the kitchen to make good food using simple ingredients that most importantly, taste delicious.

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Recipe Rating


  1. 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.

  2. 5 stars
    Absolutely the best!!! I am pre-diabetic and have been trying to follow strict diet and was desperately in need of a treat for dessert and this completely filled the spot it is totally creamy smooth and no guilt with no sugar. Thank you so much for sharing this wonderful recipe with a with the world!

  3. 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.

  4. 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!!!