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- Besti Monk Fruit Allulose Blend – I originally made these almond flour pumpkin muffins with erythritol sweetener, but updated the recipe to use Besti instead, because it makes them more moist and gives them a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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391 Comments
Melissa Jusztin
0I was craving something pumpkin. Search the internet for low carb/keto. Came across your recipe and had all the ingredients so I baked them last night. So delicious. Even my worst critic (my daughter) thought they were yummy. Had one this morning with coffee. Great way to start the day.
Maya | Wholesome Yum
0I am happy you liked the muffins, Melissa! Thanks for stopping by!
Penny Frick
0Hi Maya, Did you use cupcake liners? When I have made muffins in the past, I have used silicone liners which make for easy removal, but the sides never seem to brown like the muffin tops. I am considering just putting these in the muffin tin with just a bit of non stick baking spray. Any thoughts from you or your readers on how they have baked a successful muffin?
Maya | Wholesome Yum
0Hi Penny, I used parchment paper liners. You could try just greasing the muffin tin directly, but I haven’t tried to say for sure if it would work. Let me know how it goes for you! It would likely be easier to remove them after cooling in this case.
Karen
0I have made these muffins four times now and LOVE them! They were my first introduction to keto baking and I was amazed at how yummy they were! Thanks for all your hard work developing and taste testing these recipes!
Nita OBrien
0I just spray the muffin tin and they come lout easy and no waste sticking to the papers.
Maya | Wholesome Yum
0I am so happy you liked them, Karen! Have a great day!
Andrea
0These were really good! A little fudgy on the inside but I loved the crunch of the pumpkin seeds. Couldn’t even wait for them to cool down. Going to try some butter on it tomorrow. I love all your recipes and you are my go to for when I want to try a new low carb recipe! Thank you!
Maya | Wholesome Yum
0Thank you, Andrea! I’m glad you liked them. You can bake them for a little longer if they are too fudgy inside. If the tops are too browned but the inside isn’t done, you can tent the top with foil to finish baking. I’m so glad you like the recipes!
Laurie
0Wow! These taste unbelievable! Thank you so much for this recipe! I was hoping to get a good recipe for this thanksgiving season, and this is the one! I hope I can just stop at one. I didn’t have pumpkin seeds, so I chopped up some almonds for the crunch, tastes great.
Maya | Wholesome Yum
0I am so happy to hear that, Laurie! Thank you!
Kitti Dee
0I made these today but use pure maple syrup and stevia. I also added macadamia nuts. They were the BEST gluten-free muffins I have ever tasted!!!! Thank you for this wonderful recipe!
Maya | Wholesome Yum
0I love that, Kitti! Thank you!
Stephanie
0I’m astounded at how delicious and easy this was not to mention weight loss friendly!
I added pecans because they were on hand. I chopped some up and just eyeballed it. Put a pecan half on top. Beautiful, light and fluffy! WOW!
Thanks so much !
Maya | Wholesome Yum
0I am so happy to hear that, Stephanie! Please come back soon!
Wendy
0I made these into donuts with the addition of some Lily’s mini chocolate chips, and tipped it with a confectioners Swerve and pumpkin pie spice glaze! Super yummy!
Maya | Wholesome Yum
0I am so happy the muffins, Wendy! Thank you!
Elizabeth
0I’m obsessed with my boyfriends moms’ pumpkin muffins, but wanted something with low sugar and low carbs to enjoy them with a little less guilt! Came across this recipe and it turned out AMAZING! I threw in some 72% dark chocolate chips which sweetened it up a bit more.
Maya | Wholesome Yum
0I am so happy to hear that, Elizabeth! Thank you!
Ronda
0Made these this morning. Delicious! Couldn’t even tell they were healthy. The best pumpkin muffin recipe I’ve tried yet.
Maya | Wholesome Yum
0I am so happy to hear that, Ronda! Have a great day!
ARDwyer
0I’d like to add flax meal to this recipe. Should I swap out the almond flour or just add 1/2 flax meal?
Maya | Wholesome Yum
0You can replace either some or all of the almond flour with flax seed meal. However, the flax seed meal makes the muffins a bit more gritty/grainy after cooling. If you are nut-free, I recommend sunflower seed meal instead. If you do use flax seed meal anyway, I recommend using it for some of the almond flour replacement but not all.
Becky
0Do you think it is possible to get 12 muffins instead of 10? If so what would be the nutrition info 12 muffins? And if you added pecans what would the nutrition be? Thanks
Maya | Wholesome Yum
0Hi Becky, You could make 12 muffins, but you’d have much less “muffin top”. The baking time might be reduced a little. I don’t have nutrition info for substitutions or modifications, but if you want to change something you can enter the ingredients you use and the number of servings changed into an online calculator.
Haley
0These are fabulous!!! Definitely saving the recipe. Do you know the saturated fat content?
Maya | Wholesome Yum
0Thank you so much, Haley! I don’t have that off-hand but you can enter the ingredients you used into an online calculator.
Patti
0I made these this morning. They were very good, but for me I am going to cut back on the pumpkin pie spice. They were also VERY moist inside, I cooked them for almost 25min and they were brown on top. I let them sit for about 5 min as they seem to recommend with any Keto baking recipe.
Maya | Wholesome Yum
0I am so happy you liked the muffins, Patti! Have a great day!
Terri
0These were amazing. I doubled the recipe (to share), and added 1/4 cup of avocado oil so they would be more moist. I also used Sukrin brown sugar substituted, and reduced the amount of that by 1/3. They were delicious!
Maya | Wholesome Yum
0I love to hear that, Terri! Thank you!
Lauri
0My kitchen is filled with scents of Fall. Fresh out of the oven just minutes ago – delicious muffins! The only substitution I made – I used pure maple syrup for my sweetener and only used 1/2 cup. Otherwise, followed recipe as written. Truly DELICIOUS and nutritious. A great way to begin a chilly day.
Maya | Wholesome Yum
0Yay for Fall, Lauri! Thanks for stopping by!
Christina James
0I am allergic to coconut, so would I just replace it with the same amount of almond flour?
Maya | Wholesome Yum
0Hi Christina, No, sorry, they are not interchangeable. Coconut flour absorbs a lot of liquid, so replacing it with the same amount of almond flour would make the muffins too wet. You could try replacing the 1/2 cup coconut flour with 1 1/2 cup almond flour (yes, triple the amount), but you’d end up with a lot more muffins and I can’t say for sure if that’s the right consistency. I have a video that will be posted shortly and you can check that to see what the batter consistency should be like.
Julie
0I replaced the eggs with flax eggs and they turned out great! I did have to cook them a little extra, but all worth the wait!
Maya | Wholesome Yum
0I am so happy you liked the muffins, Julie! Have a nice day!
Marion Buller
0I’m baking these now. They definitely do not have the smooth tops like your pictures. The batter was very thick. Is there something to make them moister? I added the extra oil already.
I just took them out of the oven and they are soft and moist on the inside, a little grainy. I used Swerve powdered sweetener because it’s what I had available. Any suggestions or do I just find a new recipe?
Maya | Wholesome Yum
0Hi Marion, Yes, the batter should be thick – BUT I did update the recipe recently to make it more moist. Finally, I recommend using almond flour or sunflower seed meal over flax seed meal, due to possible issues with graininess. I hope you’ll try the current version on the recipe card. I think you’ll like it much better!
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!