Gluten-Free Keto Pumpkin Muffins

If you ask me, keto pumpkin muffins are a total game-changer for fall baking.

These low-carb treats give you all the cozy pumpkin spice flavors without the guilt. Warm cinnamon and nutmeg blend with real pumpkin puree to create that perfect autumn taste.

They’re made with almond flour instead of regular flour and sweetened with a sugar substitute that actually tastes good. A touch of cream cheese keeps them moist and fluffy.

It’s a keto-friendly dessert that doesn’t feel like you’re missing out, perfect for anyone watching their carbs but still craving something sweet.

What Kind of Pumpkin Puree Should I Use?

For these keto muffins, you’ll want to use pure pumpkin puree, not pumpkin pie filling which already has spices and sugar added. You can find canned pure pumpkin puree in the baking aisle year-round, and brands like Libby’s work perfectly fine. If you’re feeling ambitious, you can make your own by roasting a sugar pumpkin and pureeing the flesh, but honestly, the canned stuff is convenient and tastes great. Just make sure the label says “100% pure pumpkin” and doesn’t list any other ingredients like spices or sweeteners.

Options for Substitutions

These keto muffins are pretty forgiving when it comes to swaps, but a few ingredients are key to getting the right texture:

• Coconut flour: This one’s tricky to substitute since coconut flour is super absorbent. If you must swap it, try 1 cup almond flour instead, but you’ll need to add an extra egg to help bind everything together.
• Stevia glycerite: You can use other keto sweeteners like erythritol (use 1/3 cup granulated) or monk fruit sweetener (follow package directions for sugar equivalent). Liquid stevia works too – start with 1/2 teaspoon and taste as you go.
• Pumpkin puree: Make sure you’re using pure pumpkin puree, not pumpkin pie filling. In a pinch, you could try mashed butternut squash or even sweet potato puree, though the flavor will change slightly.
• Avocado oil: Any neutral oil works here – coconut oil, olive oil, or even melted butter for greasing the liners.
• Cream cheese frosting: The frosting is totally optional, but if you want to skip it or make it dairy-free, try whipped coconut cream sweetened with your preferred keto sweetener instead.

Watch Out for These Mistakes While Baking

The biggest mistake with keto pumpkin muffins is overmixing the batter once you add the coconut flour, which can make your muffins dense and gummy – just fold the ingredients together until barely combined.

Coconut flour is incredibly absorbent, so if your batter looks too thick, resist the urge to add more liquid right away; instead, let it sit for 5 minutes to allow the flour to hydrate properly.

Another common error is overbaking these muffins since they can go from perfectly moist to dry very quickly – start checking for doneness at 18 minutes with a toothpick, and remember they’ll continue cooking slightly after you remove them from the oven.

Make sure your cream cheese is truly softened for the frosting, not just room temperature, as cold cream cheese will create lumps that are hard to smooth out even with vigorous mixing.

What to Serve With Keto Pumpkin Muffins?

These keto pumpkin muffins are perfect for breakfast or an afternoon snack with a hot cup of coffee or sugar-free chai tea. Since they’re already topped with that creamy cinnamon frosting, they’re pretty complete on their own, but I love serving them alongside some crispy bacon or breakfast sausage for a more filling meal. For a cozy fall brunch, try pairing them with scrambled eggs and maybe some sliced avocado for extra healthy fats that fit right into your keto lifestyle. They also make a great dessert when served with a dollop of whipped cream or a small handful of toasted pecans for some added crunch.

Storage Instructions

Keep Fresh: These keto pumpkin muffins stay moist and delicious when stored in an airtight container at room temperature for up to 3 days. If you’ve added the cream cheese frosting, definitely keep them in the fridge for up to 5 days since dairy needs to stay cool.

Freeze: You can absolutely freeze these muffins for up to 3 months! I like to freeze them without the frosting first, then add it fresh when I’m ready to eat them. Wrap each muffin individually in plastic wrap, then pop them all in a freezer bag.

Enjoy: Frozen muffins thaw perfectly at room temperature in about 30 minutes, or you can microwave them for 20-30 seconds if you’re in a hurry. The cream cheese frosting can be made ahead and stored in the fridge for up to a week – just give it a quick stir before spreading it on your muffins.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 1100-1300
• Protein: 32-38 g
• Fat: 94-106 g
• Carbohydrates: 34-42 g

Ingredients

For the muffins:

• 1 tbsp avocado oil (for greasing muffin liners)
• 4 large eggs
• 1/2 cup pumpkin puree
• 4 tbsp unsalted butter, melted and cooled
• 1 tsp stevia glycerite (equivalent to 1/3 cup sugar)
• 2 tsp vanilla extract
• 2 tsp ground cinnamon
• 6 tbsp coconut flour (44 grams)
• 1 tsp baking powder (gluten-free optional)

For the frosting:

• 8 oz cream cheese, softened
• 1/4 cup pumpkin puree
• 1 tsp stevia glycerite (equals 1/3 cup powdered sugar)
• 1/2 tsp ground cinnamon
• 1/2 tsp vanilla extract

Step 1: Prepare the Muffin Pan and Preheat Oven

• 1 tbsp avocado oil (for greasing muffin liners)

Preheat the oven to 350°F (175°C).

Line 6 muffin cups with foil or silicone liners and grease them well with avocado oil to prevent sticking.

If using paper liners, make sure to grease them thoroughly, as muffins tend to stick more to paper.

Set aside.

Step 2: Make the Muffin Batter

• 4 large eggs
• 1/2 cup pumpkin puree
• 4 tbsp unsalted butter, melted and cooled
• 1 tsp stevia glycerite (equivalent to 1/3 cup sugar)
• 2 tsp vanilla extract
• 2 tsp ground cinnamon
• 6 tbsp coconut flour (44 grams)
• 1 tsp baking powder (gluten-free optional)

In a medium bowl, whisk together the eggs, 1/2 cup pumpkin puree, melted and cooled butter, 1 tsp stevia glycerite, vanilla extract, and ground cinnamon until fully combined.

Once the wet mixture is smooth, whisk in the coconut flour, taking your time to avoid lumps.

When the batter is very smooth, whisk in the baking powder until just incorporated.

Step 3: Portion and Bake the Muffins

• batter from Step 2

Evenly divide the muffin batter among the 6 prepared muffin cups, using a 4-tablespoon scoop for each.

Bake the muffins in the preheated oven for 22-25 minutes, or until they are set and a toothpick inserted into the center comes out clean.

Once baked, transfer the muffins to a cooling rack and allow them to cool completely before frosting.

I find that letting the muffins come to room temperature really improves their texture.

Step 4: Prepare the Pumpkin Cream Cheese Frosting

• 8 oz cream cheese, softened
• 1/4 cup pumpkin puree
• 1 tsp stevia glycerite (equals 1/3 cup powdered sugar)
• 1/2 tsp ground cinnamon
• 1/2 tsp vanilla extract

While the muffins cool, place the cream cheese, 1/4 cup pumpkin puree, 1 tsp stevia glycerite, 1/2 tsp ground cinnamon, and 1/2 tsp vanilla extract in a small bowl.

Whisk with a hand whisk or electric mixer until smooth and creamy, about 2 minutes.

I like to chill the frosting for a few minutes in the fridge before piping—it helps it hold its shape!

Step 5: Frost and Serve the Muffins

• baked and cooled muffins from Step 3
• pumpkin cream cheese frosting from Step 4

Transfer the pumpkin cream cheese frosting from Step 4 to a piping bag and pipe on top of the completely cooled muffins (from Step 3), or spread with a spatula for a rustic finish.

Enjoy immediately, or refrigerate for later.

Gluten-Free Keto Pumpkin Muffins

Delicious Gluten-Free Keto Pumpkin Muffins recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 12 minutes mins

Cook Time 24 minutes mins

Total Time 36 minutes mins

Servings 4

Calories 1200 kcal

Ingredients

  

For the muffins:

• 1 tbsp avocado oil (for greasing muffin liners)
• 4 large eggs
• 1/2 cup pumpkin puree
• 4 tbsp unsalted butter, melted and cooled
• 1 tsp stevia glycerite (equivalent to 1/3 cup sugar)
• 2 tsp vanilla extract
• 2 tsp ground cinnamon
• 6 tbsp coconut flour (44 grams)
• 1 tsp baking powder (gluten-free optional)

For the frosting:

• 8 oz cream cheese, softened
• 1/4 cup pumpkin puree
• 1 tsp stevia glycerite (equals 1/3 cup powdered sugar)
• 1/2 tsp ground cinnamon
• 1/2 tsp vanilla extract

Instructions

 

• Preheat the oven to 350°F (175°C). Line 6 muffin cups with foil or silicone liners and grease them well with avocado oil to prevent sticking. If using paper liners, make sure to grease them thoroughly, as muffins tend to stick more to paper. Set aside.
• In a medium bowl, whisk together the eggs, 1/2 cup pumpkin puree, melted and cooled butter, 1 tsp stevia glycerite, vanilla extract, and ground cinnamon until fully combined. Once the wet mixture is smooth, whisk in the coconut flour, taking your time to avoid lumps. When the batter is very smooth, whisk in the baking powder until just incorporated.
• Evenly divide the muffin batter among the 6 prepared muffin cups, using a 4-tablespoon scoop for each. Bake the muffins in the preheated oven for 22-25 minutes, or until they are set and a toothpick inserted into the center comes out clean. Once baked, transfer the muffins to a cooling rack and allow them to cool completely before frosting. I find that letting the muffins come to room temperature really improves their texture.
• While the muffins cool, place the cream cheese, 1/4 cup pumpkin puree, 1 tsp stevia glycerite, 1/2 tsp ground cinnamon, and 1/2 tsp vanilla extract in a small bowl. Whisk with a hand whisk or electric mixer until smooth and creamy, about 2 minutes. I like to chill the frosting for a few minutes in the fridge before piping—it helps it hold its shape!
• Transfer the pumpkin cream cheese frosting from Step 4 to a piping bag and pipe on top of the completely cooled muffins (from Step 3), or spread with a spatula for a rustic finish. Enjoy immediately, or refrigerate for later.