Keto Pumpkin Muffins (Gluten-Free)

These keto pumpkin muffins are soft, tender, gluten-free, and packed with warm pumpkin spice flavor. They are made with almond flour, golden flax meal, real pumpkin puree, and a sugar substitute for a low-carb muffin that tastes like fall without the sugar.

At only 1.4 net carbs per muffin, they make a great option for breakfast, brunch, an afternoon snack, or a sugar-free pumpkin treat.

If you love pumpkin season but want to keep your carbs in check, these low-carb pumpkin muffins are a simple and delicious way to enjoy those classic fall flavors.

I have an entire collection of keto muffin recipes you may want to check out.

Why You'll Love These Keto Pumpkin Muffins

These gluten-free pumpkin muffins have all the warm spices you expect from a traditional pumpkin muffin but without the refined flour or sugar.

They are:

• Keto-friendly
• Low in carbs
• Gluten-free
• Sugar-free
• Made with real pumpkin puree
• Easy to freeze
• Perfect for meal prep
• Great for fall baking

The combination of almond flour and golden flax makes these also high in fiber.

The Best Low-Carb Pumpkin Muffins

Pumpkin recipes can be tricky on keto because pumpkin does contain some natural carbs. The good news is that a little pumpkin puree goes a long way in adding flavor, moisture, and that beautiful pumpkin color.

For this recipe, I used just enough pumpkin puree to give the muffins that classic pumpkin flavor while still keeping them low in carbs.

These keto pumpkin muffins are also made without a frosting or glaze, which keeps them simple, less sweet, and perfect as a true muffin.

Ingredients 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. 

• Canned Pumpkin Puree: Be sure to use 100% canned pumpkin puree, not pumpkin pie filling. Pumpkin pie filling has added sugar and spices, which would make this recipe much higher in carbs.
• Granulated Sugar Substitute: Use your favorite granulated sugar substitute that measures cup-for-cup like sugar. This keeps the muffins sugar-free while still giving them the right level of sweetness.
• Unsalted Butter: Melted unsalted butter adds richness and helps keep the muffins moist.
• Vanilla Extract: A little vanilla helps enhance the pumpkin and warm spices.
• Eggs: Room-temperature eggs help the batter mix smoothly and give the muffins structure.
• Finely Milled Almond Flour: For the best texture, use finely milled almond flour, not almond meal. Almond meal is coarser and can make the muffins heavier.
• Golden Flax Meal: Golden flax meal is important for this recipe because it helps add fiber and structure while keeping the muffins tender. I do not recommend using regular flax meal because it can give the muffins a gummy texture and affect the final crumb. Golden flax meal also has a milder flavor that pairs nicely with the warm pumpkin spices.
• Baking Powder: Baking powder helps the muffins rise and gives them a lighter texture.
• Pumpkin Spices: This recipe uses cinnamon, ginger, nutmeg, and cloves for that classic pumpkin spice flavor.
• Sea Salt: A little salt balances the sweetness and brings out the flavors.
• Chopped Walnuts: Walnuts are optional, but they add a nice crunch and pair beautifully with pumpkin.

How To Make Keto Pumpkin Muffins

To make these muffins, start by preheating your oven to 400 degrees and lining two muffin tins with liners. Since this recipe makes 18 muffins, you will need more than one standard muffin pan.

In a large mixing bowl, beat the pumpkin puree, sugar substitute, melted butter, and vanilla extract until well combined. Then add the eggs one at a time, making sure each egg is fully incorporated before adding the next.

Next, add the almond flour, golden flax meal, baking powder, cinnamon, ginger, nutmeg, cloves, and sea salt to the wet ingredients. Mix until everything is fully combined. The batter will be thick, and that is exactly what you want.

Fold in the chopped walnuts if you are using them.

Divide the batter evenly among the prepared muffin cups, filling each about ¾ full.

Bake the muffins at 400 degrees for the first 5 minutes. Then, without removing the muffins from the oven, reduce the temperature to 350 degrees and continue baking until the muffins are golden and an inserted toothpick comes out clean.

Allow the muffins to cool in the pan for about 10 minutes before transferring them to a baking rack to cool completely.

How To Get Rounded Muffin Tops

Starting the muffins at a higher oven temperature helps give them a quick lift. Baking them at 400 degrees for the first 5 minutes allows the batter to rise before the temperature is reduced.

After those first 5 minutes, lower the oven temperature to 350 degrees without removing the muffins from the oven. This helps them finish baking evenly without overbrowning.

Since keto muffins do not rise the same way traditional wheat-based muffins do, this simple method helps create a fuller, more rounded muffin top.

For best results, divide the batter evenly among the muffin cups and avoid underfilling them.

Tips For The Best Gluten-Free Pumpkin Muffins

For the best results, be sure to use 100% pumpkin puree, not pumpkin pie filling.

Pumpkin pie filling contains added sugar and other ingredients that are not keto-friendly.

You will also want to use finely milled almond flour instead of almond meal, since a finer flour gives these muffins a softer, better crumb.

Once the dry ingredients are added, mix the batter just until everything is fully combined. Overmixing can make the muffins more dense.

Keep in mind that keto muffin batter is often thicker than traditional muffin batter, especially when using almond flour and golden flax meal, so do not be alarmed by the texture.

Sweetener Options

For this keto pumpkin muffin recipe, I recommend using a granulated sugar substitute that measures cup-for-cup like regular sugar.

A monk fruit and erythritol blend or allulose blend work well.

If you prefer a stevia based sweetener, I recommend you reduce the amount by half since it is doubly sweet.

Check out our keto sweetener guide for a more detailed explanation.

How To Store Keto Pumpkin Muffins

Store leftover muffins in an airtight container in the refrigerator for up to 5 days.

You can enjoy them chilled, bring them to room temperature before serving, or warm them slightly in the microwave.

These muffins freeze well. Once the muffins have cooled completely, place them in a freezer-safe container or freezer bag and freeze for up to 3 weeks.

For best results, thaw them in the refrigerator overnight or on the counter before serving.

More Keto Pumpkin Recipes

If you enjoy these low-carb pumpkin muffins, be sure to check out more of our keto pumpkin recipes. Pumpkin is one of those flavors that makes sugar-free baking feel extra special, especially during the fall season.

Tag Us

I sure hope you'll give this recipe a try. When you do, be sure to tag us on Instagram and Facebook. It truly encourages me to keep sharing and perfecting these keto recipes for you.

You can also visit our Amazon Store for some of our favorite keto baking tools, pantry staples, and low-carb recommendations.

Grab Our Books & Recipe App

In case you don't know, we've authored two keto cookbooks, Essential Keto Bread and Essential Keto Desserts, both inspired by your requests over the years.

You can also find even more easy keto recipes for breakfast, lunch, dinner, snacks, and desserts inside the  Fit to Serve Group App on  iOS and Android.

Join Our Jesus And Keto Movement

Looking for support on your keto journey? We invite you to join our private Jesus and Keto Facebook group, where we encourage one another to pursue lasting transformation through faith, grace, and a low-carb lifestyle.

Be sure to also request our FREE Jesus and Keto E-Book: First 7 Days. We pray it blesses you.