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 drastically change. Long gone were the days when I would make a pumpkin recipe oozing with sweetness.
Yay for being keto-adapted. It’s pretty remarkable how your body begins to desire 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 also visit.
And if you are a fan of pumpkin recipes, don’t forget to also check out our keto pumpkin recipes.

Keto Pumpkin Cream Cheese Cupcakes
The fact remains that once pumpkin season rolls around this girl gets a major hankering for pumpkin treats. And it seems like I can’t stock up enough on pumpkin puree cans.
I just get all caught up with the flavors of the season and somehow find myself making something pumpkin all the time. Thankfully, my family is not complaining and actually encourages me to keep testing recipes on them.
These low-carb pumpkin cupcakes came out of a need to create something festive that would be easy to transport. Seems like it’s that time of year when treats and invites abound.
So I wanted to be able 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 too, because these lovelies, also make the best snack, dessert, and even quick breakfast.
How To Make Keto Cream Cheese Cupcakes

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Filled with the warm spices of fall and packed with pumpkin flavor you will be able to enjoy these cupcakes all pumpkin season long and not feel deprived.
With just a few basic keto baking staples you will be 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 then sift for best results.
It really is worth that little extra step to get the perfect texture when keto baking. 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.
Keto Pumpkin Muffins With Cream Cheese Frosting

When I started out to create this recipe I knew one thing was certain, and that’s that, I wanted the pumpkin and spices flavor to be pronounced.
It’s why you’ll see that I was generous when it came time to add spices. I’ve topped these low carb pumpkin cupcakes with both a cream cheese frosting and a little drizzle of sugar-free caramel sauce that’s totally optional since these muffins can stand alone be just as delicious.
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The app is loaded with hundreds of yummy recipes for breakfast, lunch, dinner, snacks, and even desserts!
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Keto Pumpkin Cream Cheese Cupcakes
Enjoy a rich-tasting keto pumpkin cream cheese cupcakes recipe that is low in carbs, sugar-free, gluten-free, grain-free and keto-friendly option.
Ingredients
Keto Pumpkin Cream Cheese Cupcake Batter
- 1 1/2 cups of finely milled almond flour, measured and sifted
- 1 1/2 tablespoons of ground cinnamon
- 1 1/2 teaspoons ground ginger
- 1/8 teaspoon ground clove
- 1 1/2 teaspoon baking powder
- 1/4 teaspoon sea salt
- 1/2 cup of unsalted butter, room temperature
- 4 ounces of full-fat cream cheese, room temperature
- 3/4 cup of granulated sugar-substitute, I used Lakanto
- 1/4 cup of brown sugar-substitute, I used Lakanto Gold
- 1 teaspoon of vanilla extract
- 3 large eggs, room temperature
- 1/2 cup pumpkin puree, unsweetened pumpkin puree
Keto Cream Cheese Frosting
- 3/4 cup confectioner's sugar-substitute, I used Lakanto Powdered
- 1/2 teaspoon of vanilla extract
- 1/4 cup of unsalted butter, room temperature
- 3-4 tablespoons of heavy whipping cream
- 4 ounces of full-fat cream cheese, softened
Instructions
Keto Pumpkin Cream Cheese Cupcakes
- Pre-heat oven to 365 degrees.
- Line two 12 capacity muffin tin pan with cupcake liners.
- In a medium-sized bowl measure, sift together the almond flour, spices, baking powder and set aside.
- Next in another medium-sized bowl using an electric mixer beat the softened butter, cream cheese both sugar substitutes, vanilla extract. Beat until light and creamy about 2 minutes.
- To this mix add the pumpkin puree and mix just until well incorporated.
- Next add the eggs one at a time, alternating with the dry ingredients mixing thoroughly after each addition.
- Pour the cupcake batter evenly into the muffin pan.
- Bake for about 18-25 or until an inserted toothpick comes out clean.
- Wait until the cupcakes are fully cool, at least 1/2 hour before adding the cream cheese frosting.
Keto Cream Cheese Frosting
- Beat the cream cheese and butter until light and fluffy using an electric mixer.
- To this add gently add the confectioners sugar-substitute.
- Next, add the heavy whipping cream a couple of tablespoons at a time and beat until fully combined.
- Set aside until cupcakes are fully cooled before frosting.
Notes
Store leftovers in the refrigerator for up 5 days. You can freeze the cupcakes for up to 3 weeks but they must not be frosted to do so.
Optional: Decorate the frosted cupcakes with a drizzle of Lakanto caramel sauce and a few pieces of chopped walnuts.
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Nutrition Information:
Yield: 24 Serving Size: 1Amount Per Serving: Calories: 225Total Fat: 21.5gSaturated Fat: 8.9gTrans Fat: 0gCholesterol: 110mgSodium: 129mgCarbohydrates: 4.6gNet Carbohydrates: 2.3gFiber: 2.3gSugar: 1gProtein: 6.9g