Keto Pumpkin Cream Cheese Cupcakes

If you’re a fan of pumpkin cupcakes but need a healthier version, then this recipe for keto pumpkin cream cheese cupcakes has your name on it.

The good thing is that these sugar-free pumpkin cream cheese muffins are low in carbs, grain-free, gluten-free, sugar-free, and keto-friendly. Really, can it get any better?

These cupcakes are super moist, flavor-packed, and topped with the perfect amount of cream cheese frosting. 

I’ve always looked forward to pumpkin season, but when I went low-carb keto, things had to change drastically. Long gone were the days when I would make a pumpkin recipe oozing with sweetness and gluten.

I am thrilled to report that these pumpkin cupcakes have the best texture and use simple ingredients!

Yay for being keto-adapted! It’s pretty remarkable how your body desires less sugar once you remove it from your diet.

Besides this recipe for low-carb pumpkin cream cheese cupcakes, I have a complete list of Keto Cakes that I encourage you to visit.

If you are a fan of pumpkin recipes, don’t forget to check out our keto friendly pumpkin recipes.

Keto Pumpkin Cream Cheese Cupcakes 

Once pumpkin season rolls around, this girl gets a significant craving for pumpkin treats. And it seems like I can’t stock up on enough pumpkin puree cans.

I get all caught up with the season’s flavors and somehow find myself making something pumpkin all the time. 

Thankfully, my family is not complaining and encourages me to keep testing recipes on them.  

These low-carb pumpkin cupcakes were inspired by the need to create something festive and easy to transport. It seems like that time of year when treats and invitations abound.

So, I wanted to have a keto-friendly treat that would also make a great host gift. 

That’s not to say that these delightful muffins shouldn’t be enjoyed at home, either. They also make the best snacks, desserts, and even quick breakfasts.

It’s a great option for pumpkin lovers who want to silence their sweet tooth while following a keto lifestyle. The best part is that these clock in at only 2.3 g net carbs per cupcake! 

Ingredients & Tools Needed

Disclosure: Some of the links below are affiliate links, meaning, at no additional cost to you, I will earn a commission if you click through and make a purchase.

Note that the full printable recipe card is at the bottom of the page.

Keto Pumpkin Cream Cheese Cupcake Batter

• Finely milled almond flour
• Ground cinnamon
• Ground ginger
• Ground clove
• Baking powder
• Sea salt
• Unsalted butter, room temperature
• Full-fat cream cheese, room temperature
• Granulated sugar-substitute
• Brown sugar-substitute
• Vanilla extract
• Large eggs, room temperature
• Pumpkin puree, unsweetened pumpkin puree

Keto Cream Cheese Frosting

• Confectioner’s sugar-substitute
• Vanilla extract
• Unsalted butter, room temperature 
• Heavy whipping cream
• Full-fat cream cheese softened

Tools Needed

• Muffin pan
• Muffin cups (cupcake liners)
• Electric Mixer or hand mixer
• Mixing bowls
• Cooling rack

How To Make These Cupcakes

These cupcakes are filled with the warm spices of fall and pumpkin flavor, so you can enjoy them all pumpkin season long without feeling deprived.

With just a few basic keto baking staples, you will be able to create cupcakes you’ll be proud to serve.

My flour of choice for these muffins is finely milled almond flour, and I recommend you measure and then sift for the best results.

Getting the perfect texture when keto baking is worth that little extra step. 

As far as sweeteners are concerned, I used Lakanto’s monk fruit classic granulated and Gold, which is their brown sugar substitute.

And for the cream cheese frosting, I used Lakanto’s confectioner’s sugar sub (powdered). You could, of course, use your favorite sweeteners, but I thought I would share my favorite since I get the most consistent results when I use them.

I start by preheating my oven to 365 degrees and lining two 12-capacity muffin tin pans with cupcake liners.

I measure and sift the almond flour, spices, and baking powder in a medium bowl and set it aside.

In another medium-sized bowl, I use an electric mixer to beat the softened butter, cream cheese, sugar substitutes, and vanilla extract until the mixture is light and creamy, which takes about 2 minutes.

Once that’s done, I add the pumpkin puree and mix until it’s well incorporated. Then, I add the eggs one at a time, alternating with the dry ingredients, making sure to mix thoroughly after each addition.

I pour the cupcake batter evenly into the muffin pan and bake for about 18-25 minutes, or until a toothpick inserted comes out clean.

After baking, I let the cupcakes cool completely for at least half an hour before I prepare the cream cheese frosting.

For the frosting, I beat the cream cheese and butter with an electric mixer until light and fluffy.

I gently add the confectioner’s sugar substitute to the mixture, followed by the heavy whipping cream and a couple of tablespoons, beating until everything is thoroughly combined.

I set the frosting aside until the cupcakes are thoroughly cooled, ready to be frosted, and enjoyed.

Keto Pumpkin Muffins With Cream Cheese Frosting

When I began to create this recipe, I knew one thing: I wanted the pumpkin and spice flavors to be pronounced.

That’s why you’ll see I was generous when it came time to add spices.

I’ve topped these low-carb pumpkin cupcakes with cream cheese frosting and a slight drizzle of sugar-free caramel sauce, which is totally optional since these muffins can stand alone and be just as delicious.

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Once you do, make sure you remember to tag us on Instagram and Facebook. It’s what keeps this girl encouraged to keep sharing and perfecting her recipes.

Grab Our Books!

In case you don’t know, we have authored two books for you, Essential Keto Bread and Essential Keto Desserts, both inspired by your requests over the years.

I pray these keto cookbooks will help make keto a delicious breeze for you.

Join Our Jesus And Keto Movement 

Looking for an online support system to help you stay on keto? As a family, we came to the keto diet, looking at it from a Christian perspective. As believers, we live our lives supported by God’s grace.

So when the Holy Spirit led us to combine our Christian faith and the keto diet, we did so in hopes of finding lasting transformation. When we followed the Holy Spirit’s prompting, we got on the path to real transformation. 

Knowing firsthand the benefits of this decision, we have created a closed Christian group that is using the keto diet to transform their lives.  We invite you to join our Private Facebook Group and see if it’s not the key you have been missing.

Be sure to request our FREE Jesus and Keto E-Book (First 7 Days). We hope it blesses you.

Fittoservegroup Keto App

Looking for a fast way to access our keto recipes? We’ve got you covered. There’s an app for that. Yup, there’s a Fit To Serve Group App, and it’s going to make your keto diet a delicious breeze!

Access hundreds of recipes that are all sugar-free, gluten-free, and keto-friendly.

Enjoy early access to recipes on the website before they go live. Plus, there are bonus recipes that are exclusive to the app. Make your own personal cookbooks that you can use to organize your favorite recipes.

Search recipes by title, ingredients, keywords, and categories, and of course, every recipe shows complete nutritional facts.  Get the Fit to Serve Group App for easy-to-follow keto recipes made with easy-to-source ingredients.

The app is loaded with hundreds of yummy recipes for breakfast, lunch, dinner, snacks, and even desserts!

Learn more by visiting our Fit To Serve Group App Page.