These soft, fluffy keto pumpkin muffins are made with almond flour and pumpkin pie spice, then topped with a maple cream cheese frosting and a caramelized pecan. They're the perfect low carb treat for fall, and they're sugar free and gluten free too!

It's that time of year when everything is all about pumpkins and pumpkin pie spice! And what could be better than a pumpkin muffin?
These muffins are made with canned pumpkin puree, and just like my low carb pumpkin cookies, the result is a very soft and fluffy treat. I've topped them with a creamy maple cream cheese frosting and a caramelized pecan. It's a fantastic combination, and it looks cute too.
As usual with muffins and cupcakes, I only make a small batch of six. I find that if I have too many hanging around, I'm prone to overindulging! Each muffin comes out at 5g net carbs, so you'll want to share them. If you have a bigger family than mine, the recipe doubles easily.
Key Ingredients & Substitutions
- Pumpkin puree. Use plain canned pumpkin that says 100% pure pumpkin on the label, like Libby's 100% Pure Pumpkin. Don't grab pumpkin pie filling by mistake; it looks almost the same on the shelf, but it's already sweetened with sugar and spiced, which would send the carbs way up. The recipe uses 8 ounces, which is about half of a 15-ounce can.
- Almond flour vs coconut flour. I bake these with blanched almond flour, which gives a tender, moist crumb and a mild nutty flavor that goes so well with pumpkin. Coconut flour behaves very differently: it soaks up a lot more liquid, so you can't swap it cup for cup. See the FAQ below if you'd like to use coconut flour only.
- Monk fruit or stevia sweetener. I use Lakanto Classic Monk Fruit Sweetener, which measures like sugar. A granulated stevia blend such as Pyure Organic Stevia Blend works too, but it's sweeter than sugar, so start with about half the amount and taste the batter. Pure liquid stevia isn't a good swap here because it adds no bulk to the batter.
- Heavy cream and egg. The cream keeps the batter rich and moist, and the single egg holds everything together. Full-fat canned coconut milk can stand in for the cream if you're out.
- Pumpkin pie spice. A ready-made blend like Simply Organic Pumpkin Pie Spice is easiest. To make your own, mix cinnamon with a little ginger, nutmeg and a pinch of cloves.
- Frosting ingredients. Softened cream cheese, heavy cream, a powdered sweetener like Lakanto Powdered Monk Fruit Sweetener (granulated would make the frosting gritty), and a sugar-free maple syrup. ChocZero Sugar Free Maple Syrup is my go-to, or try Lakanto Sugar Free Cinnamon Maple Syrup for a little extra spice.
- A tip for moist muffins. Almond flour muffins dry out when they're overbaked, so start checking at 22 minutes and take them out as soon as the tops spring back. Let them cool in the pan for 10 minutes before moving them, and once they're cold, keep them covered so they don't lose moisture.
How to Make Keto Pumpkin Muffins
Add the pumpkin puree (make sure it is 100% pumpkin), heavy cream, sweetener, almond flour, egg, pumpkin pie spice and vanilla extract to a stand mixer or a mixing bowl.

Beat until smooth. It only takes about a minute.

Line a six-hole muffin pan with silicone liners, and divide the pumpkin mixture between them.

Bake in a preheated 375°F oven for 25 minutes or until cooked through, then leave to cool completely.
To make the maple cream cheese frosting, beat together the softened cream cheese, powdered sweetener, heavy cream and low carb maple syrup until smooth. If you love a thicker, pipeable topping, my low carb cream cheese frosting works here too.

Spread the frosting over the cooled muffins. A flat spatula or palette knife is the perfect tool!

Finally, decorate each one with a caramelized pecan. I have two different methods for you: the skillet version in my Low Carb Pumpkin Mousse recipe, or these slow cooked Low Carb Caramelized Pecans!
Helpful Tips
Blot very wet pumpkin. Some brands of canned pumpkin are much looser than others. If yours looks watery, spread it on a couple of paper towels for a few minutes before measuring so the muffins bake up fluffy instead of dense and gummy in the middle.
Fill the liners well. This batter doesn't rise much, so fill the liners almost to the top. Silicone liners are great here because the muffins pop right out and nothing gets left stuck to paper.
Don't frost them warm. Cream cheese frosting melts and slides off warm muffins. Give them a full hour to cool, or pop them in the fridge for 20 minutes if you're short on time.
Soften the cream cheese first. Cold cream cheese leaves little lumps in the frosting. Leave it on the counter for 30 minutes, or microwave it for 10 seconds, before you beat it with the other frosting ingredients.
Double the batch the easy way. Everything doubles neatly, including the egg, so you can make twelve muffins in a standard 12-cup pan. Keep the bake time the same, but start checking a couple of minutes early.

Variations
- Cream cheese swirl. Skip the frosting and bake the cream cheese right in. Beat 2 ounces of softened cream cheese with 1 tablespoon of powdered sweetener and a few drops of vanilla, spoon a teaspoon onto each filled liner, and swirl it in with a toothpick before baking. It's a great way to get pumpkin cream cheese muffins you can grab on the go.
- Chocolate chips. Stir a small handful of sugar-free chocolate chips, like Lily's Dark Chocolate Baking Chips, into the batter. Pumpkin and chocolate are a lovely pairing, and the kids won't complain!
- Pecan streusel. Mix 2 tablespoons almond flour, 2 tablespoons chopped pecans, 1 tablespoon melted butter, 1 tablespoon granulated monk fruit sweetener and a pinch of cinnamon. Sprinkle it over the batter before baking and leave off the frosting.
- Extra spiced. Add an extra half teaspoon of cinnamon and a pinch of ground ginger for a bolder pumpkin spice flavor.
- Walnut crunch. Swap the caramelized pecan on top for toasted walnut halves, or fold a tablespoon of chopped walnuts into the batter.
Serving Ideas
These muffins are just right with a cup of coffee for a cozy weekend breakfast, or tucked into a lunchbox as an afternoon treat. For a fall brunch, serve them with scrambled eggs and bacon and add a batch of keto banana muffins so everyone gets a choice.
They also make an easy dessert for Halloween or Thanksgiving gatherings. Arrange them on a platter with some keto pumpkin fat bombs, and nobody will guess the whole spread is sugar free.
Storing & Freezing
Because the frosting is made with cream cheese, frosted muffins belong in the fridge. Keep them in an airtight container for up to 4 days, and let them sit at room temperature for 10 to 15 minutes before eating so the crumb softens up again. Unfrosted muffins will keep in an airtight container on the counter for a day, or in the fridge for up to 5 days.
For freezing, it's best to freeze the muffins without frosting. Wrap each cooled muffin in plastic wrap, then put them all in a freezer bag for up to 3 months. Thaw them overnight in the fridge or on the counter for about an hour, then frost and add the pecans. You can also warm a thawed, unfrosted muffin in the microwave for 10 to 15 seconds.
The frosting can be made up to 3 days ahead and kept covered in the fridge. Give it a quick stir before spreading it.
FAQs
Are pumpkin muffins keto?
Regular bakery pumpkin muffins aren't, because they're made with wheat flour and sugar. These ones are keto friendly: they use almond flour, a monk fruit sweetener and sugar-free maple syrup, and pumpkin itself is fairly low in carbs when you're only using 8 ounces across six muffins.
How many net carbs are in a pumpkin muffin?
Each frosted muffin in this recipe has about 5g net carbs (7g total carbs minus 2g fiber) and 165 calories. The monk fruit sweetener isn't counted, since it has no net carbs. A typical bakery pumpkin muffin can easily have 50g of carbs or more.
Can I make these with coconut flour only?
Yes, but it isn't a straight swap. Coconut flour absorbs far more moisture than almond flour, so use about 2 tablespoons of coconut flour in place of the ½ cup of almond flour, add a second egg, and let the batter rest for 5 minutes to thicken before filling the liners. The muffins will be a little more cake-like and slightly smaller. Treat this as a starting point rather than a tested swap, and check them a few minutes early.

More Low Carb Pumpkin Recipes
If you loved these muffins, here are a few more pumpkin treats you might enjoy:
- Low Carb Pumpkin Cookies
- Low Carb Pumpkin Pie Crème Brûlée
- Keto Pumpkin Ice Cream (with Candied Bacon)
- Low Carb Carrot Cake Muffins
- Low Carb Halloween Recipes
📖 Recipe

Keto Pumpkin Muffins (Low Carb!)
Ingredients
Equipment
Step-by-Step Instructions
- Preheat the oven to 375°F (190°C) and line a six-hole muffin pan with silicone liners.
- Add the pumpkin puree, almond flour, Lakanto, heavy cream, egg, pumpkin pie spice and vanilla extract to a mixing bowl. Beat with a stand mixer or hand mixer on medium speed for about 1 minute, until smooth.
- Divide the batter evenly between the six liners (they will be quite full). Bake for 25 minutes, until the tops are golden and spring back when lightly pressed and a toothpick inserted in the center comes out clean.
- Leave the muffins in the pan for 10 minutes, then move them to a wire rack and let them cool completely, about 1 hour. Frosting melts on warm muffins.
- To make the maple cream cheese frosting, beat the softened cream cheese, powdered sweetener, heavy cream and low carb maple syrup together until smooth and creamy.
- Spread the frosting over the cooled muffins with a flat icing spatula and top each one with a caramelized pecan.
- Store frosted muffins in an airtight container in the fridge for up to 4 days.
Nutrition
Notes
Tried this recipe?
Let us know how it was!Nutritional information is provided as a courtesy and is my best approximation. Net carbs are calculated as the total grams carbs minus the total grams of fiber.





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