Keto Pumpkin Cheesecake Cupcakes

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These Keto Pumpkin Cheesecake Cupcakes are perfectly soft, creamy, and loaded with delicious pumpkin flavor. Enjoy sugar-free mini pumpkin cheesecakes that are just 3 grams of net carbs each.

mini keto pumpkin cheesecake recipe

Fall is here, and I’ve been waiting impatiently to pull out the pumpkin and start sharing some pumpkin recipes with you. I’ve made some exciting recipes ahead of time, and I have got some delectable recipes for this fall that are sure to impress everyone.

I love these mini keto pumpkin cheesecakes because you can make them the night before, place them in the refrigerator overnight, and dessert is ready to go the next day. Top them with my decadent keto caramel sauce for the best experience.

Why Are You Going to Love These Keto Pumpkin Cheesecake Cupcakes

  • quicker to make than regular cheesecake
  • They are low carb and keto  One serving contains only 3 grams of net carbs!
  • Instead of regular sugar, these keto-friendly cupcakes use keto sweetener.

Ingredients For Keto Pumpkin Cheesecake Cupcakes

For these delicious low carb pumpkin cheesecake cupcakes, you need just a few simple ingredients that are cheap and very accessible: 

For The Crust:

  • Almond Flour – Almond flour is one of the best keto flour. It’s low-carb, packed with protein, healthy monounsaturated fats, and other essential nutrients like Vitamin E and Manganese. And most importantly, it works great as a flour substitute.
  • Sweetener – When it comes to sweeteners, you can choose your favorite one. Mine are Eryhtitol, Allulose, or Monk Fruit. For the crust, I used granular erythritol.
  • Butter – Gives that great buttery flavor to the crust.
  • Salt – Salt helps to balance the tastes and keeps your muffins from becoming overly sugary.

For The Filling 

  • Cream Cheese – Softened full-fat cream cheese is the key in this recipe.
  • Sweetener – for the filling, I use a powdered sweetener as it blends easily.
  • Eggs – They act as a binder and soften the texture of our muffins.
  • Vanilla Extract – For a boost of flavor.
  • Pumpkin Puree –  Make sure that your pumpkin puree contains only one ingredient: Pumpkin. If you’re not sure which one to get, we are here to help you. Take a look at our guide on How to Roast Pumpkin and Make Pumpkin Puree.
  • Pumpkin Pie Spice – The key is to use a mix that does not have any added sugar. Or you can make your mix at home.
easy mini pumpkin cheesecakes

How To Make Keto Pumpkin Cheesecake Cupcakes

Following these simple steps, these almond flour pumpkin cheesecake cupcakes bites will completely satisfy your sweet tooth and definitely impress your guests.

We’ll start by making the crust for our mini keto pumpkin cheesecakes: 

  1. Add all the dry ingredients to a mixing bowl. Stir them together, making sure to get all the lumps out. Then add the melted butter and mix well to combine.
  2. Divide between 12 cupcakes.
  3. Bake them for about 5-8 minutes until it starts to brown.

Make The Filling:

  1. To make the cheesecake filling, you’ll want to start with cream cheese at room temperature. If your cream cheese is too cold, it will be lumpy, and mixing will not remove the lumps.
  2. Mix all the ingredients in a bowl except the pumpkin.
  3. Use 2/3 of the cream to fill the cupcake pan. Add pumpkin puree and pumpkin pie spice to the remaining cream cheese mixture and combine well.
  4. To assemble the cheesecakes, add a layer of cheesecake filling and top with the pumpkin mixture.
  5. Bake them until a toothpick can be poked into the center and come out cleanly for about 20-25 minutes.
keto pumpkin mini cheesecake

Tips For Making Keto Pumpkin Cheesecake Cupcakes

  • Room temperature ingredients always ensure a smoother and creamier filling without lumps.
  • It is a great idea to separate your dry ingredients from your liquid ingredients while mixing, and that’s because you don’t want to have any lumps in your muffins.

How To Store These Keto Pumpkin Cheesecake Cupcakes

  • These Keto Pumpkin Cheesecake Cupcakes can be stored nicely in the fridge for about a week. Simply place them in an airtight container and, if possible, towards the back of the refrigerator.
  • If you want to freeze them, place the cupcakes on a clean plate, then wrap tightly with plastic wrap before placing them in a ziplock bag. Freeze for up to a month; any longer will cause the flavor and texture to deteriorate. When you want to eat them, make sure to take them out of the freezer a few hours before consuming them.
best pumpkin cheesecake single serving

Tools You Need To Use

Another great thing is that you don’t need many tools to make these Keto Pumpkin Cheesecake Cupcakes. Here’s all you need:

  • Spatula
  • Measuring Cups
  • Mixing Bowl
  • Muffins Pan
  • Muffins Liners
sugar free keto mini pumpkin cheesecakes

Looking For More Keto Pumpkin Recipes? Try these:

mini keto pumpkin cheesecake recipe

Keto Pumpkin Cheesecake Cupcakes

5 from 3 votes

Prep time 15 minutes
Cook Time 20 minutes
Yelds 16 servings
Author Ioana Borcea from LowCarbSpark.com


These Keto Pumpkin Cheesecake Cupcakes are perfectly soft, creamy, and loaded with delicious pumpkin flavor. Enjoy sugar-free mini pumpkin cheesecakes that are just 3 grams of net carbs each.
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Pumpkin Cheesecake Layer


  • Preheat oven to 350°F/180°C.
  • Make the crust: In a large bowl, whisk together almond flour, melted butter, sweetener, cinnamon, and a pinch of salt.
  • Divide the crust mixture among 16 muffin cups lined with muffins liners. Firmly press about a tablespoon of the crust mixutre.
  • Bake in the preheated oven for 5-8 minutes or until golden brown.
  • Make the filling: In a large mixing bowl, add room temperature cream cheese, eggs, powdered sweetener, vanilla extract, pumpkin pie spice, cinnamon, and salt. Use an electric mixer to blend together until smooth and creamy.
  • Take 1/3 of the filling and mix it with pumpkin until well combined.
  • Pour the cheesecake filling over each cooked crust, then top with a tablespoon of the pumpkin mixture.
  • Bake for 20-25 minutes or until the tops look nearly set but still soft to touch.
  • Remove from the oven and allow to cool, then refrigerate for at least 2 hours.
  • Serve with homemade keto caramel sauce and a pinch of sea salt. Whipped cream or pecans are great toppings too.
Nutrition Facts
Amount per serving.
Total Carbs
Net Carbs

How do we calculate the nutrition info?

These nutrition facts listed are determined using nutrition information from the USDA Food Database. Our nutrition facts are accurate, but if you are using different products, please make your calculations. Net carb count is calculated by subtracting both fiber and sugar alcohols because they don’t raise blood sugar.

Course Dessert
Cuisine American
Keyword mini pumpkin cheesecake
Tried this recipe?Mention @LowCarbSpark or tag #LowCarbSpark!
Keto Pumpkin Cheesecake Cupcakes


The full recipe is in the recipe card below. Readers that love this aslo made these recipes:


Ioana is a food and travel lover. Her greatest passion is developing mouthwatering recipes that are comforting, easy to make, and budget friendly! She firmly believes that cooking should be fun! About me...

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Hello! My name is Ioana Borcea, and I'm here to provide you with mouthwatering recipes. This blog is all about sharing my favorite tested easy to make, delicious low-carb & keto, nutrient-dense recipes.

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