Keto Pumpkin Cheesecake Cupcakes

This post contains affiliate links, and we may receive a small commission if you purchase through our site.

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 the 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 keto pumpkin cheesecake
  • They are low carb and keto  One serving contains only 3 grams of net carbs!
  • These cupcakes can be made ahead of time, which is great for meal prep or when expecting guests.
  • Crowd-Pleaser: Everyone loves these cupcakes, making them a hit at social gatherings and family events.
  • Festive: They’re perfect for holidays, especially Halloween, Thanksgiving, and Christmas when pumpkin-flavored treats are especially popular.

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 ErythritolSwerveMonk Fruit, or Allulose. For the crust, I used granular erythritol.
  • Butter – Gives that great buttery flavor to the crust.
  • Salt – Salt helps to balance the taste 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 (my favorite!) 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 try my homemade pumpkin pie spice.
easy mini pumpkin cheesecakes

How To Make Keto Pumpkin Cheesecake Cupcakes

Following these simple steps, these almond flour pumpkin cheesecake cupcake 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: 

In a mixing bowl, add the dry ingredients – the almond flour, sweetener, cinnamon (if using), and a pinch of salt. Pour the melted butter over the dry ingredients. Use a spatula or a wooden spoon to mix well until all of the dry ingredients are moistened by the butter and the mixture starts to come together.

Line a 12-cup muffin pan with parchment paper liners or use silicone muffin cups to prevent sticking. Evenly divide the crust mixture using a spoon or a cookie scoop.

Press down firmly on the mixture in each muffin cup to form a solid base for your cheesecakes. The back of a spoon or the bottom of a small glass can be used to press down evenly.

Bake them for about 5-8 minutes until it starts to brown.

Make The Filling:

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.

Mix all the ingredients in a bowl except the pumpkin.

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.

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.
  • When making the cheesecake mixture, use a low to medium speed to avoid incorporating too much air into the cheesecake. Too much air can cause your cupcakes to rise too quickly and then fall, leaving them with cracks.
  • Ensure you’re using pure pumpkin puree, not pumpkin pie filling which contains added sugars and spices that are not keto-friendly.
  • Cheesecakes are often set as they cool, so take them out of the oven when the centers are just slightly jiggly. Overbaking can lead to cracks and a dry texture.

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

To prepare the keto pumpkin cheesecake, you’ll need a set of common kitchen tools. Here’s a list to help you get everything ready:

  • 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 10 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.
Keto during holidays?
Get my e-book!



Pumpkin Cheesecake Layer


  • Preheat the oven to 350°F/180°C.
  • Make the crust: In a large bowl, combine the almond flour, sweetener, melted butter, cinnamon, and a pinch of salt. Whisk together until well mixed.
  • Line 16 muffin cups with muffin liners. Divide the crust mixture among the lined muffin cups, pressing about a tablespoon of the mixture firmly into the bottom of each cup.
  • Bake the crusts in the preheated oven for 5-8 minutes, or until they are just starting to turn golden brown. Keep a close eye on them to prevent burning.
  • Make the filling: In a large mixing bowl, use an electric mixer to blend the cream cheese, powdered sweetener, eggs, vanilla extract, pumpkin pie spice, and cinnamon until smooth and creamy.
  • Take 1/3 of the cheesecake filling and mix it with the pumpkin puree 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 are nearly set but still slightly soft in the center.
  • Remove from the oven and let them cool at room temperature. Once cooled, refrigerate the cheesecakes for at least 2 hours to allow them to set completely.
  • Serve with homemade keto caramel sauce and a pinch of sea salt. Whipped cream or candied pecans are great toppings too.


Make sure your pumpkin puree is unsweetened and not pumpkin pie filling, which has added sugars.
Watch the crust closely as it bakes since almond flour can burn quickly. It should be just turning golden.
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!


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...

Leave a Question, comment or review!

Your email address will not be published.

Required fields are marked *

Recipe Rating

About me

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.

Connect with us on Social Media

Do not use the contents of this website as medical or nutrition advice. This website is only intended for informational and educational purpose.

LowCarbSpark.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to amazon.com.

Copyright © 2015-2024 LowCarbSpark. All Rights Reserved.