Bake Healthier This Fall With My Almond Flour Pumpkin Muffins

When I first made these almond flour pumpkin muffins, I started with a much simpler version: less pumpkin, no milk, and even a different sweetener. They were good, but a little dry. After re-testing (and plenty of cozy fall breakfasts at my house), I found that adding more pumpkin puree, a splash of almond milk, and swapping in Besti made them so much softer and more moist. Here’s why I keep making them every fall:
- Soft and moist, with all the pumpkin flavor – Between the real pumpkin puree, cozy pumpkin pie spice, and my blend of clean-ingredient flours, these almond flour pumpkin muffins are super moist and taste like pure fall in every bite.
- I feel good about eating them – These are refined sugar free, gluten free, and naturally low carb and keto, with a dairy free option. I feel light after eating them.
- Easy to customize – I like sprinkling pumpkin seeds on top, but chocolate chips, walnuts, or pecans also work well. The almond flour base keeps the muffins sturdy enough for add-ins. And, I’ve even got an idea below for a creamy filling!
So grab a can of pumpkin, warm up your oven, and make these almond flour pumpkin muffins with me!


Reader Review
“This is the best pumpkin muffin recipe I have EVER made! It’s moist and fluffy and everything you could want in a pumpkin treat.” –Carol
⭐⭐⭐⭐⭐
Ingredients & Substitutions
Here I explain the best ingredients for my almond flour pumpkin muffins recipe, what each one does, and substitution options. For measurements, see the recipe card.
- Wholesome Yum Almond Flour – My finely milled almond flour gives the best texture. If you need nut-free, sunflower seed meal works better than flaxseed meal, but almond flour still has the best flavor and crumb. I don’t recommend using almond meal, which is more coarse and will make your muffins grainy.
- Wholesome Yum Coconut Flour – This is key here because pumpkin adds so much moisture, and the absorbent coconut flour soaks up the excess. But if you want to make these pumpkin muffins with almond flour alone, you can replace the coconut flour with an extra 1 1/2 cups of almond flour. (Yes, it’s quite a bit more.)
- Besti Monk Fruit Allulose Blend – I originally made these almond flour pumpkin muffins with erythritol sweetener, but updated the recipe to use Besti instead, because it makes them more moist and gives them a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. That’s because Besti locks in moisture and makes muffins softer! Other sweetener options (like ones labeled “monk fruit” or “stevia”) typically contain erythritol as well, so will make these more dry. I also reduced the sweetener amount from 2/3 cup to 1/2 cup, based on reader feedback and my own re-testing. I don’t recommend using a liquid sweetener because it’ll make the batter too wet; make my regular almond flour muffins instead if you want to use a liquid one.
- Pumpkin Puree – I usually grab canned to save time. Just be sure it’s plain puree, not pumpkin pie filling with added sugar. This recipe doesn’t use the whole can, so you can save the extras to make my pumpkin banana bread. You can certainly roast your own pumpkins (I recommend sugar pie pumpkins if you do this) if you have time.
- Pumpkin Pie Spice – I like using my homemade pumpkin spice blend of cinnamon, nutmeg, ginger, cloves, and allspice, but store-bought works fine.
- Eggs – Bind the batter and give structure. Feel free to substitute flax eggs.
- Milk – I usually use almond milk (plain or vanilla both work), but have had success using coconut milk beverage (the kind in a carton, not the thick canned one) and even regular dairy milk.
- Ghee – I used this as a dairy-sensitive option for a friend. You can use unsalted butter if you like, or coconut oil for a completely dairy-free version.
- Baking Powder, Vanilla Extract, and Sea Salt – Don’t confuse baking powder with baking soda, they are not the same!
- Add-Ins – I used pumpkin seeds (pepitas) this time, but have also enjoyed walnuts, pecans, or sugar free dark chocolate chips.
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How To Make Pumpkin Muffins With Almond Flour
I have step-by-step photos here to help you visualize the recipe. For full instructions with amounts and temperatures, see the recipe card.
- Mix the dry ingredients. In a large bowl, whisk together the almond flour, coconut flour, Besti, baking powder, pumpkin pie spice, and sea salt. I used a spatula in my picture below, but these days prefer a whisk because it breaks up clumps without requiring me to sift ingredients.
- Add the wet ingredients. Crack in the eggs, then stir in the pumpkin puree, almond milk, melted ghee (or your fat of choice), and vanilla. The batter will be thicker than a classic muffin batter.


- Scoop the batter. Use a spoon to divide the pumpkin muffin batter into a lined muffin tin. I like to add a sprinkle of pepitas for crunch.
- Bake in the preheated oven. These almond flour pumpkin muffins are ready when the tops are golden and a toothpick comes out clean.

My Tips For The Best Texture
- Use room temperature ingredients. They’ll mix more smoothly. Plus, cold almond milk or eggs can solidify your melted ghee.
- Expect a thicker batter, and don’t thin it out. The combo of pumpkin and coconut flour naturally makes the batter thicker. Your muffins won’t set properly if you add extra liquid.
- Some readers prefer an extra 1/2 cup of almond flour. These almond flour pumpkin muffins turn out firmer that way, but personally I prefer them as written with an extra moist texture.
- A lighter-colored muffin tin works best. I bake mine in this USA-made muffin pan, because it doesn’t get the muffins as dark. It also cleans up really easily in case of any batter spills.
- For the photos, I used parchment liners, but lately I’ve been using silicone ones. I like these because they have notches to help lift them out.
- Fill the liners almost to the top. Almond flour and coconut flour don’t rise like wheat flour does, so I make sure the cups are nice and full.
- Watch the bake time. Ovens can vary, so while mine take about 25 minutes, I start checking at 22. Pull them as soon as a toothpick comes out clean so they stay moist.
- If the tops are browning too quickly, just tent the pan loosely with foil. That way they can finish baking without getting darker.
- It’s normal for the tops come out a little flat. You can see that in my pictures here. They still taste moist and fluffy!
- Cooling on a wire rack improves the inner texture. I always let my almond flour pumpkin muffins cool before enjoying, but do usually reheat them in the microwave or the oven. And a pat of butter on a warm muffin is just perfect!
- Want a more dessert-like vibe? You can add the filling from my cinnamon cream cheese muffins here, or just pipe cream cheese frosting on top after baking.


Almond Flour Pumpkin Muffins
My almond flour pumpkin muffins are moist, sweet, and naturally low carb and gluten-free. A feel-good, cozy bite of fall in every bite!
Instructions
[ See step photos See my tips ]Tap on the times in the instructions to start a kitchen timer.
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Preheat the oven to 350 degrees F (177 degrees C). Line 10 muffin cups with parchment liners (I use this muffin tin).
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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.
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Stir in the the eggs, pumpkin puree, almond milk, melted ghee, and vanilla, until completely incorporated.
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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.
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Bake for about 25 minutes, until an inserted toothpick comes out clean and the muffins are very slightly golden around the edges.
Did you make it? Leave a review or tag me @wholesomeyum on Instagram!
Maya’s Recipe Notes
Serving size: 1 muffin
- Recipe update: I updated this recipe to make the muffins more moist. 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.
- Tips: Check out my recipe tips above to help you get the best texture in these almond flour pumpkin muffins, plus my favorite dessert-like variation.
- Storage: I usually keep these in a covered container on the counter for 2–3 days, or the fridge up to a week.
- Freeze: Keep them in the freezer for up to 3 months. Thaw on the counter, or you can reheat from frozen with a little butter or coconut oil.
📖 Want more recipes like this? Find this one and many more in my Fall Ebook Bundle!
I provide nutrition facts as a courtesy. Have questions about calculations or why you got a different result? Please see my nutrition policy.
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Almond Flour Pumpkin Muffins

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393 Comments
Aron
0I made these today and they’re fantastic! I saw the recipe on your site a few months ago, but wanted to wait to make them until it was closer to fall weather. I love pumpkin anything. These are soft and moist, and they have a great pumpkin flavor. Thanks for sharing all these wonderful ideas!
Maya | Wholesome Yum
0I am so happy you liked them, Aron! Have a great day!
Lexi Sickafoose
0These were so yummy! I’m ready for fall!!! My kids loved them too! Thank you!
Maya | Wholesome Yum
0I am so happy you and your kids liked the muffins, Lexi! Have a great day!
Ashley
0I made these last night and they’re perfect! I made them with butter instead of ghee, and used only 1 teaspoon of baking powder. I used a leveled ice cream scoop to fill the cups and got exactly 10 muffins.
The flavor is amazing, this is the best low carb recipe I’ve made yet!
Maya | Wholesome Yum
0I am so happy that you liked them, Ashley! Thanks for stopping by!
Jean
0I tried these but all I could taste was the baking powder. Can I reduce or not even use it?
Maya | Wholesome Yum
0Hi Jean, Did you by chance use baking soda instead of baking powder? They aren’t the same, and baking soda would have a strong taste. Baking powder is different, and necessary to make the muffins rise.
Jessica Beatty
0If using erythritol, wouldn’t the sugar be less than 2g, bringing the net carbs significantly down? This recipe looks awesome and I cannot wait to try it.
Maya | Wholesome Yum
0Hi Jessica, No, the nutrition info is already based on using erythritol. The small amount of carbs comes from the other ingredients (pumpkin, almond flour and coconut flour).
Aimee
0This recipe is awesome!! You nailed the texture by using almond flour and coconut flour together. They were moist but not gummy. This will be in my regular rotation. Thanks!
Maya | Wholesome Yum
0I am so happy you liked it, Aimee! Have a nice day! Please come back again soon!
Valerie Baker
0These are really good. I added more butter and pumpkin puree to get them a little more runny, and they turned out great, really yummy with a dollop of butter and warmed in microwave. I think these would be really good with a streusal topping.
Maya | Wholesome Yum
0I am so happy you liked the muffins, Valerie! Thanks for stopping by!
Rachael Ross
0I’m going to try these but for the sweetener… is it granular or confectioner’s? Thanks!
Maya | Wholesome Yum
0You use granular erythritol in this recipe, Rachael! I hope you like them!
Nichol
0My daughter and i just recently started this low carb way of eating and we have been experimenting on new ideas to curb our cravings. Tried your recipe tonight because I love pumpkin everything. These are to die for!!! Do you think this could be made into a bread?! Definitely hit the spot! Thank you so much.
Maya | Wholesome Yum
0Thank you so much, Nichol! I’m glad you like them. I haven’t tried these as a bread but I’m sure you can – you’d just need to bake it for longer. You may need to tent the top with foil if it browns before the inside is done. I also have a separate pumpkin bread recipe here you can try.
Lindsay
0These were incredible! My super picky 7 year old loved them too. The recipe is perfect. Thanks so much 🙂
Maya | Wholesome Yum
0I am so happy you and your 7 year old liked the muffins, Lindsay!
Tammi J Riley
0The pumpkin muffins are amazing! Very moist even without adding extra butter.
Maya | Wholesome Yum
0I am so happy you liked the pumpkin muffins, Tammi!
Joy
0Well they smell great. I can’t wait to see how well they turn out. You’re recipe was very easy. Thank you!
Maya | Wholesome Yum
0I hope they taste as delicious as they smell, Joy!
Alice
0I was able to get 12 medium sized muffins from the recipe cutting the net carb down to 2g! I also added a tablespoon of low carb brown sugar sweetener hoping to get that molassesy flavor! Fingers crossed!
Maya | Wholesome Yum
0Let me know how you like them, Alice! Have a great day!
Mystel Winters
0Hi Maya! I ADORE your website and recipes 🙂 I tried these this morning, and noticed though that the batter was super thick – more like cookies instead of muffins. It may be my fault for using coconut oil instead of ghee, because I’ve noticed that ghee is liquid at room temperature but coconut oil is solid. Anyhow, I added too much *extra* liquid to the batter and the muffins turned out really soft, but they taste amazing, so I don’t mind the softness 😉 Thank you for a great nut free recipe!
Maya | Wholesome Yum
0Hi Mystel! I am so happy you liked them! I hope to see you back soon!
Deena Jones
0Delish!. I tried it with one less egg since most of the low carb baked goods tend to taste too “eggy” in my opinion. They turned out just fine, but my batter only made 7 muffins.
I filled the cups of the tin completely full, so that may account for the lesser number of finished product. Also, 20 minutes at 350 was perfect for the one less egg batter.
I will try adding in walnuts or sliced almonds next time.
Thanks for the recipe!
Maya | Wholesome Yum
0Walnuts and almonds sound like wonderful additions, Deena!
Charlene Miller
0These are perfect! I threw in 1/2 cup each of raisins and walnuts for while I’m at work…. delicious!! Thanks for a great recipe!
Maya | Wholesome Yum
0I love your additions, Charlene! I am so happy you liked them!
Chris
0How long will they stay good on the counter?
Maya | Wholesome Yum
0Hi Chris, They will stay good on the counter for a few days. They keep in the fridge for a bit longer beyond that, and you can also freeze them if you want to.
Helene Denny
0Hi Maya, I like your gluten-free recipes. Question – what can I use to substitute eggs in your bread or cookie recipes?
Maya | Wholesome Yum
0Thank you, Helene! Substitutions would depend on the recipe. For this one I have not tested it without eggs, but you might be able to do it using flax eggs instead. Let me know how it goes if you try!
Cindy
0These are the best muffins! They are a regular go-to recipe for me. I bake a lot with Erythritol since trying to stay away from sugar, and find it to be very satisfying. Thank you so much for posting the recipe.
Maya | Wholesome Yum
0Thank you, Cindy! I’m glad you like them!
Brenda
0This is a great recipe. I added a tsp of xanthan gum, seemed to make them not as “heavy”, made 8 muffins and baked them 20 min. I keep them in a plastic container in the fridge with a bowl of cream cheese that has been whipped with whipping cream, a bit of sweetener and a dash of cinnamon right beside to use as a spread!
Maya | Wholesome Yum
0Thank you, Brenda! That spread sounds delicious!