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Low carb pumpkin recipes are one of the best things about fall! Especially healthy, low carb keto pumpkin muffins. These are deceptively simple, but taste so rich and cozy — most people won’t believe they’re coconut and almond flour pumpkin muffins! They’re made with real food ingredients and no sugar whatsoever.

If you love pumpkin recipes this time of year, be sure to also try pumpkin pie cupcakes and sugar-free pumpkin bread.

Which flour is the best one to use for healthy pumpkin muffins? Naturally, as with all my keto desserts, I only considered low carb flours. I experimented on keto pumpkin muffins with almond flour, coconut flour, and flax seed meal. Almond flour alone can be too heavy, coconut flour is too dense, and flax seed meal can be a little gritty. In the end, I settled on a combination of almond flour and coconut flour.

Making the low carb pumpkin muffins with coconut flour and almond flour helps create the best texture, better than one or the other alone. The coconut flour also helps keep them lighter. Low carb coconut flour recipes tend to be less heavy than almond flour ones.

In particular, I use a blend of Wholesome Yum Almond Flour, Coconut Flour, and Besti Monk Fruit Allulose Blend for the batter — the allulose keeps them super soft and moist, while the mix of flours keeps them cake-like. They make the ultimate pumpkin keto muffins that anyone can enjoy, whether or not they’re keeping track of carbs.

Why You’ll Love This Low Carb Keto Pumpkin Muffins Recipe

  • Rich pumpkin spice flavors
  • Moist, cakey texture
  • Uses basic keto baking ingredients
  • Just 10 minutes prep time
  • About 4 grams net carbs per muffin
Almond flour pumpkin muffins in a muffin tin

Almond Flour Pumpkin Muffins Ingredients

This section explains how to choose the best ingredients for keto pumpkin spice muffins, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.

  • Wholesome Yum Almond Flour – This flour creates naturally gluten free pumpkin muffins, and it’s finely milled for a more authentic texture.
  • Wholesome Yum Coconut Flour – This flour is made from one ingredient (pure organic coconuts!) and helps absorb the extra moisture from the pumpkin. Don’t skip it!
  • Besti Monk Fruit Allulose Blend – This sweetener helps the muffins bake up soft, all with 0g net carbs. You may be able to substitute erythritol or another keto sweetener here, but the taste and texture will be different.
  • Baking Powder
  • Pumpkin Pie Spice – This is a blend of spices, including ground cinnamon, ginger, nutmeg, cloves, and allspice. You can get it pre-mixed or make homemade pumpkin pie spice instead.
  • Sea Salt
  • Eggs – Use whole, large eggs.
  • Pumpkin Puree – You can make your own or get it canned. Avoid getting canned pumpkin pie filling, which contains added sugar.
  • Almond Milk – Either plain or vanilla is fine, but make sure it’s unsweetened. You can order it online, get it at the grocery store, or make homemade almond milk. Other types of keto friendly milk would also work fine here.
  • Ghee – Ghee makes these paleo pumpkin muffins, but you can also use butter or coconut oil instead. I admit I usually use butter when I make these.
  • Vanilla Extract
  • Pumpkin Seeds – These are pepitas, the hull-less seeds from specific varieties of pumpkins. Avoid seeds with the hull, which can be tough to chew in this recipe. You could easily swap these with walnuts, pecans, or sugar free chocolate chips, or top with a layer of cream cheese frosting after baking.

See the variations section below if you want to make these nut-free, dairy-free, paleo, or with cream cheese filling.

Low carb pumpkin muffins ingredients

How To Make Low Carb Almond Flour Pumpkin Muffins

This section shows how to make keto friendly pumpkin muffins with step-by-step photos and details about the technique. For full instructions, see the recipe card below.

  • Mix dry ingredients. In a large mixing bowl, combine flours, sweetener, baking powder, pumpkin pie spice, and sea salt. Whisk well to ensure no clumps.
Mixing dry ingredients for low carb pumpkin muffins
  • Add wet ingredients. Add eggs, pumpkin puree, almond milk (or keto milk of choice), ghee (or fat of choice), and vanilla. Mix until completely incorporated. (It will be thicker than a traditional muffin batter — this is normal.)
Keto pumpkin muffin batter in a bowl
  • Scoop. Spoon the batter into a muffin tin lined with paper liners. Smooth the tops and sprinkle with pepitas.
Keto pumpkin muffins before baking
  • Bake. Bake in a 350 degree F oven until golden and an inserted toothpick comes out clean.
Baked keto pumpkin muffins in a muffin tin

Tips For The Best Low Carb Pumpkin Muffins

Making keto pumpkin muffins with almond flour and coconut flour looks a little different than using traditional white flour, so keep these tips in mind.

  • Choose the right fat. Go with ghee, butter, or solid coconut oil (melted). Avoid fats that are liquid at room temperature (i.e. olive or avocado oil), since the muffins will take on a different texture.
  • Expect a thick batter. These keto pumpkin muffins need a thicker batter than most muffin recipes, even low carb muffin recipes. (For example, low carb keto blueberry muffins have a thinner batter.) But, because of the way the pumpkin and coconut flour interact with each other, this one starts out thicker. Don’t worry, the muffins won’t be dry!
  • Fill muffin liners close to the top. Almond flour and coconut flour don’t rise as much as wheat flour, so the muffin liners should be pretty full. If you only fill them 1/2 or 3/4 of the way, you won’t get much of the best part – the muffin tops!
  • Ensure doneness. An inserted toothpick should come out clean. Underbaking the muffins can cause them to fall (deflate) or be too wet inside. If muffins are browning too quickly, you can tent the pan with foil until they’re done.
  • Cool if possible. This is not required, but cooling improves the inner texture. I do usually reheat them in the microwave or the oven when ready to eat. Adding a pat of butter to a warm muffin is just perfect!
Split open almond flour pumpkin muffin with a pat of butter


One of my favorite things about this low carb pumpkin muffin recipe is that it’s easy to customize to make additions or fit any dietary restrictions. Below are the most common ones people ask me for.

Nut-free variation:

  • Sub the almond flour: When I first published this low carb pumpkin muffins recipe, I said that golden flaxseed meal is a great almond flour replacement if you are nut-free due to allergies, or need to send these muffins to a nut-free school with your kid. However, I have since revised my recommendation and much prefer sunflower seed meal instead. It is also nut-free, but creates a much better texture than the flaxseed meal. That being said, almond flour still makes the best keto pumpkin muffins in terms of texture and flavor.
  • Sub the almond milk: Replace it with coconut milk beverage — the liquid kind in the dairy section, not the thick kind in a can.

Dairy-free or paleo variation:

Although I make lots of paleo recipes, I wasn’t really planning to make paleo pumpkin muffins in this case. Fortunately, I was pleased that they turned out that way. Virtually all the ingredients are already paleo friendly!

  • For the sweetener: Allulose is a natural sweetener, but some people prefer not to use it while following a paleo lifestyle. If that’s you, no problem. You can easily use another granulated sweetener in your paleo pumpkin muffins, like coconut sugar. That would not be sugar-free, but is natural and paleo friendly.
  • For the fat: This recipe uses ghee as the fat, which is often okay for most dairy sensitivities, but coconut oil works fine if you need to be more strict. I personally am not dairy-free, so I often use butter. Both ghee and coconut oil would be paleo friendly as well.

If your version of healthy pumpkin muffins needs to be vegan, that’s not really my thing so I highly recommend these vegan pumpkin muffins instead. She has a gluten-free variation, and you can swap the sugars with sugar-free sweeteners if you’d like.

Keto Pumpkin Cream Cheese Muffins:

These almond flour pumpkin muffins go perfectly with the cream cheese filling I made for my keto cinnamon cream cheese muffins recipe. Simply follow the recipe below to make the batter, then click the link for instructions on assembling with the cream cheese filling. (You’ll get a few extra muffins if you add filling, compared to the ones without filling.)

Storage Instructions

  • Store: Store this keto pumpkin spice muffin recipe in a covered container on the counter for 2-3 days, or in the refrigerator for up to one week.
  • Freeze: Store in a freezer-safe container. Thaw at room temperature before serving.
Keto friendly pumpkin muffins on a white surface

More Low Carb Pumpkin Recipes

If you like keto coconut flour pumpkin muffins, you’ll love these other low carb ways you can use pumpkin:


Reader Favorite Recipes

The recipe card is below! Readers that made this also viewed these recipes:

Low Carb Keto Pumpkin Muffins Recipe

Bake up low carb keto pumpkin muffins so rich and moist, you won’t believe they have 4g net carbs each! And, these almond flour pumpkin muffins are ready in 35 minutes.

Prep Time 10 minutes

Cook Time 25 minutes

Total Time 35 minutes

Servings 10 muffins


Tap underlined ingredients to see where to get them. Please turn Safari reader mode OFF to view ingredients.

Keto Sweeteners


Tap on the times in the instructions below to start a kitchen timer while you cook.

  1. Preheat the oven to 350 degrees F (177 degrees C). Line 10 muffin cups with parchment liners.

  2. In a large bowl, stir together the coconut flour, almond flour, sweetener, baking powder, pumpkin pie spice, and sea salt. Make sure there are no clumps.

  3. Stir in the the eggs, pumpkin puree, almond milk, melted ghee, and vanilla, until completely incorporated.

  4. Spoon the batter evenly into the muffin cups and smooth the tops. (They should be almost full, not 2/3 or 3/4 full.) If desired, sprinkle pumpkin seeds on top and press gently.

  5. Bake for about 25 minutes, until an inserted toothpick comes out clean and the muffins are very slightly golden around the edges.

Recipe Notes

Serving size: 1 muffin

  • This recipe was updated to make more moist muffins. The original version had 1/3 cup ghee, 1/2 cup pumpkin puree, and no almond milk. The ingredient list above and photos show the updated version.
  • I originally made these low carb pumpkin muffins with erythritol sweetener, but updated the recipe to use Besti instead, because it makes them more moist and gives them a much better texture. The sweetener amount was also reduced from 2/3 cup sweetener to 1/2 cup, based on reader feedback.

Video Showing How To Make Low Carb Pumpkin Muffins:

Tap here to jump to the video for this recipe — it’s located directly above the ingredients list. It’s the easiest way to learn how to make Low Carb Pumpkin Muffins!

Nutrition Facts

Amount per serving. Serving size in recipe notes above.

Calories 193

Fat 16.2g

Protein 5.8g

Total Carbs 7.6g

Net Carbs 4g

Fiber 3.6g

Sugar 1.4g

Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.

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Keto pumpkin muffin recipe pin