These keto pumpkin cupcakes with cream cheese frosting are moist, warmly spiced, and packed with the flavors of pumpkin pie while remaining completely sugar-free.
Made with almond flour, pumpkin puree, cream cheese, and a blend of cinnamon, ginger, and cloves, these cupcakes have a soft, tender crumb that makes them perfect for pumpkin season.
The sugar-free cream cheese frosting adds just the right amount of sweetness without overpowering the pumpkin and spices. Best of all, each frosted cupcake has only 2.3 grams of net carbs.
Serve them at a fall gathering, bring them to Thanksgiving dinner, or keep a batch in the refrigerator whenever you are craving an easy keto pumpkin dessert.
Be sure to visit our complete collection of keto pumpkin recipes for even more sugar-free ways to enjoy pumpkin season.
Why You Will Love These Keto Pumpkin Cupcakes
These low-carb pumpkin cupcakes give you all the seasonal flavor you expect from a traditional pumpkin dessert without the sugar, wheat flour, or high carb count.
They are:
- Moist and tender
- Filled with pumpkin pie spices
- Topped with sugar-free cream cheese frosting
- Made with simple keto baking ingredients
- Gluten-free and grain-free
- Only 2.3 grams of net carbs each
- Easy to transport and share
The recipe also makes 24 cupcakes, making it a great option for fall parties, church gatherings, holiday celebrations, and family dinners.
Pumpkin Pie Flavor in Cupcake Form
These cupcakes have the familiar combination of pumpkin, cinnamon, ginger, and cloves that makes pumpkin pie so irresistible.
Unlike custard-style keto pumpkin pie cupcakes, these have the soft crumb and structure of a traditional cupcake. The pumpkin puree keeps them moist, while the cream cheese and butter give the batter richness.
Once they are topped with the sugar-free cream cheese frosting, every bite has a delicious balance of pumpkin, spice, and creamy sweetness.
You can also add a light drizzle of sugar-free caramel sauce and a few chopped walnuts for an extra special fall presentation.
Ingredients & Tools Needed
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Note that the full printable recipe card is at the bottom of the page.
Keto Pumpkin Cupcakes
- 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
Optional Toppings
For a decorative finish, you can also use:
- Sugar-free caramel sauce
- Chopped walnuts or pecans
- A light dusting of cinnamon or pumpkin pie spice
Tools Needed
- Muffin pan
- Muffin cups (cupcake liners)
- Electric mixer or hand mixer
- Mixing bowls
- Cooling rack
Use Pumpkin Puree, Not Pumpkin Pie Filling
Be sure to use 100 percent pumpkin puree for these keto pumpkin cupcakes.
Pumpkin pie filling is already sweetened and usually contains sugar, spices, and additional ingredients that are not suitable for a keto recipe.
Plain canned pumpkin puree gives you control over the sweetness and spices while adding moisture and pumpkin flavor to the cupcake batter.
Choosing the Best Almond Flour
Finely milled almond flour produces the softest and most cake-like texture.
Avoid using almond meal, which contains larger pieces of the almond skin and can make the cupcakes heavier and more coarse.
For the most accurate results, measure the almond flour and then sift it with the spices, baking powder, and salt. This removes lumps and helps the dry ingredients blend evenly into the batter.
Best Sugar Substitutes for Pumpkin Cupcakes
For the cupcake batter, I use a combination of a granulated monk fruit sweetener and a brown sugar substitute.
The brown sugar substitute adds a deeper flavor that pairs especially well with pumpkin and fall spices. A granulated sugar substitute provides the remaining sweetness without adding unnecessary moisture to the batter.
Allulose can also be used, although cupcakes made with allulose may brown more quickly and have a softer texture. Begin checking them toward the lower end of the baking time.
For the cream cheese frosting, always use a powdered or confectioners' sugar substitute. A granulated sweetener can leave the frosting with a gritty texture.
If you prefer to use a stevia-based sweetener, reduce the amount by half, since it is twice as sweet as the sweetener called for in the recipe.
How To Make These Pumpkin Keto Cupcakes
Begin by preheating the oven to 365 degrees and lining two standard muffin pans with cupcake liners.
Measure and sift the almond flour, cinnamon, ginger, cloves, baking powder, and salt into a medium bowl. Set the dry ingredients aside while you prepare the wet mixture.
Using an electric mixer, beat the softened butter, cream cheese, granulated sugar substitute, brown sugar substitute, and vanilla until the mixture is creamy and lighter in texture.
Add the pumpkin puree and mix until it is evenly incorporated.
Next, add the eggs one at a time, alternating with portions of the dry ingredients. Mix after each addition, but stop once everything is fully combined. Overmixing can make almond flour cupcakes more dense.
Divide the batter evenly among the cupcake liners and bake until the tops are set and a toothpick inserted in the center comes out clean.
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Allow the cupcakes to cool completely before frosting them. Adding cream cheese frosting while they are still warm can cause the frosting to soften or melt.
How to Make Sugar-Free Cream Cheese Frosting
Beat the softened cream cheese and butter with an electric mixer until the mixture is smooth, creamy, and fluffy.
Add the powdered sugar substitute gradually, mixing on low speed at first so it does not scatter out of the bowl.
Mix in the vanilla extract. Add the heavy whipping cream one tablespoon at a time until the frosting reaches a smooth, spreadable consistency.
Once the cupcakes are completely cool, spread or pipe the frosting over the tops.
The frosting will soften at room temperature, so keep the finished cupcakes refrigerated until shortly before serving.
Tips for the Best Low-Carb Pumpkin Cupcakes
Bring the Refrigerated Ingredients to Room Temperature
Room-temperature butter, cream cheese, and eggs combine more easily and help create a smoother batter.
Cold ingredients may leave small pieces of butter or cream cheese throughout the mixture.
Measure the Almond Flour Carefully
Spoon the almond flour into the measuring cup and level it rather than packing it firmly. Too much almond flour can make the cupcakes dry or heavy.
Do Not Overmix the Batter
Once the flour has been incorporated, mix only until no dry patches remain.
Divide the Batter Evenly
Use a cookie scoop or measuring cup to divide the batter among the cupcake liners. Even portions help all the cupcakes finish baking at approximately the same time.
Allow the Cupcakes to Cool Completely
Almond flour baked goods continue to set as they cool. Giving the cupcakes enough cooling time improves their texture and prevents the frosting from melting.
How to Store Keto Pumpkin Cupcakes
Because these cupcakes are topped with cream cheese frosting, they need to be stored in the refrigerator.
Place them in a covered container and refrigerate them for up to five days. For the best texture, allow a cupcake to sit at room temperature for approximately 15 minutes before serving.
Do not leave frosted cupcakes sitting at room temperature for extended periods.
Can You Freeze Pumpkin Cupcakes?
The cupcakes can be frozen for up to three weeks, but I recommend freezing them without the cream cheese frosting.
Allow the cupcakes to cool completely and place them in a freezer-safe container with parchment paper between the layers.
Thaw them overnight in the refrigerator, then bring them to room temperature and add freshly prepared cream cheese frosting before serving.
Low-Carb Pumpkin Cupcake Variations
These keto pumpkin cupcakes are delicious as written, but you can easily change the toppings to create different fall desserts.
For added crunch, sprinkle chopped walnuts or pecans over the cream cheese frosting.
For caramel pumpkin cupcakes, drizzle the tops lightly with a keto-friendly caramel sauce.
You can also dust the frosting with cinnamon or pumpkin pie spice for a simple finish.
For unfrosted pumpkin cupcakes, leave off the cream cheese frosting and enjoy them as a lightly sweetened snack. Keep in mind that the nutritional information will change when the frosting is omitted.
Frequently Asked Questions
Traditional pumpkin cupcakes are usually made with wheat flour and sugar, making them too high in carbohydrates for a ketogenic diet.
These cupcakes use almond flour and sugar substitutes, allowing each frosted cupcake to have only 2.3 grams of net carbs.
Yes. These keto pumpkin cupcakes are made with almond flour and contain no wheat flour, making them naturally gluten-free and grain-free.
When cooking for someone with a serious gluten sensitivity, check that all packaged ingredients are certified gluten-free and have not been exposed to cross-contamination.
You can serve them without the frosting for a more muffin-like treat. However, the batter was developed as a sweet cupcake batter, so they will still have a softer and sweeter texture than a traditional breakfast muffin.
Yes. You can replace the individual cinnamon, ginger, and cloves with pumpkin pie spice.
Because spice blends vary by brand, adjust the quantity according to how strongly spiced you prefer your cupcakes.
Cream cheese frosting can become too soft when the butter or cream cheese is overly warm or when too much heavy cream is added.
Add the cream one tablespoon at a time and stop when the frosting is thick enough to spread or pipe. If it becomes too soft, refrigerate it briefly before decorating the cupcakes.
More Keto Pumpkin Recipes
Looking for more ways to use pumpkin puree? Be sure to explore our complete collection of keto-friendly pumpkin recipes, including pumpkin cakes, breads, muffins, cheesecakes, cookies, and pies.
These recipes make it possible to enjoy pumpkin season while keeping your desserts gluten-free, sugar-free, and low in carbohydrates.
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Keto Pumpkin Cupcakes With Cream Cheese Frosting
These moist keto pumpkin cupcakes are made with almond flour, pumpkin puree, cream cheese, and warm fall spices, then topped with a rich sugar-free cream cheese frosting. They are gluten-free, grain-free, and have only 2.3 grams of net carbs per cupcake.
Ingredients
Keto Pumpkin Cupcake Batter
- 1 ½ cups of finely milled almond flour, measured and sifted
- 1 ½ tablespoons of ground cinnamon
- ⅛ teaspoon ground clove
- 1 ½ teaspoons ground ginger
- 1 ½ teaspoon baking powder
- ¼ teaspoon sea salt
- ½ cup of unsalted butter, room temperature
- 4 ounces of full-fat cream cheese, room temperature
- ¾ cup of granulated sugar-substitute
- ¼ cup of brown sugar-substitute
- 1 teaspoon of vanilla extract
- 3 large eggs, room temperature
- ½ cup pumpkin puree, unsweetened pumpkin puree
Keto Cream Cheese Frosting
- ¾ cup confectioner's sugar-substitute
- ½ teaspoon of vanilla extract
- ¼ cup of unsalted butter, room temperature
- 3-4 tablespoons of heavy whipping cream
- 4 ounces of full-fat cream cheese, softened
Instructions
Keto Pumpkin Cupcakes With Cream Cheese Frosting.
- Preheat oven to 365 degrees.
- Line two 12-capacity muffin tin pans with cupcake liners.
- Measure and sift the almond flour, spices, and baking powder into a medium bowl, then set aside.
- Next, in another medium-sized bowl, using an electric mixer, beat the softened butter, cream cheese, both sugar substitutes and vanilla extract until light and creamy, about 2 minutes.
- Add the pumpkin puree to this mix and mix until it is well incorporated.
- Next, add the eggs one at a time, alternating with the dry ingredients, mixing thoroughly after each addition.
- Divide the cupcake batter evenly among the lined muffin cups.
- Bake for about 18-25 or until an inserted toothpick comes out clean.
- Wait until the cupcakes are fully cool, at least 30 minutes 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 mixture, gently add the confectioners' sugar-substitute.
- Next, add the heavy whipping cream a couple of tablespoons at a time and beat until thoroughly 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 sugar-free caramel sauce and a few pieces of chopped walnuts.
Nutrition Information:
Yield:
24Serving 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
masgautsen says
They look delicious!
fittoservegroup says
Thanks, those who tried liked them. So that's a great thing in my book ?
deborahcrocker says
Going to have to try these
fittoservegroup says
Hi Deborah ? thanks for stopping by ?
deborahcrocker says
Been sick , computer issues, but glad to read your post
fittoservegroup says
Love you Deb will keep you in my prayers
deborahcrocker says
Also I'm guilty of procrastination and easily distracted. But it's so good to hear from you all.
I appreciate and value your prayers. I'm presently seeking Gods direction and guidance over another venture. And I want to use this gift of weight loss that He graciously gave to me to bring Him honor and not to focus on me but Him. Seeking, thank you for your prayers.
fittoservegroup says
Keep us posted and email me if you want to chat and I could be of any assistance as you wait on God's direction ?
deborahcrocker says
Thank you. I just may do that.
deborahcrocker says
I canned some pumpkin couple of years ago. It actually taste good a la natural with a little sweetener. And to think its a vegetable. Amazing.
fittoservegroup says
Canning how cool is that! I have only ventured in fermenting veggies and making my own kefir. ?
deborahcrocker says
It's not to be about me me me, but it is to be about Him Him Him
fittoservegroup says
Amen well said!
BunKaryudo says
Yummy!
veezybell says
Pumpkins and cream cheese = heaven.
fittoservegroup says
?can't argue there! Enjoy!
Michele says
deborahcrocker, I love the idea of canning your own pumpkin and I'd love to have instructions for that. Did you create your own recipe or use one you found elsewhere? I would love for you to send me those instructions. I've not done a lot of canning so have no idea how to go about canning pumpkin. I have a pumpkin sitting on my dining room table and my husband has planted more, although they don't seem to be doing very well right now. But I plan on having more next year. I love pumpkin.
fittoservegroup says
Make sure you share Michelle you success!