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- Besti Monk Fruit Allulose Blend – I originally made these almond flour pumpkin muffins with erythritol sweetener, but updated the recipe to use Besti instead, because it makes them more moist and gives them a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.
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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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385 Comments
Rebecca Caldwell
0I always make pumpkin spice muffins in the fall and winter but the recipe I use is not Keto friendly. I have loved every wholesome yum recipe I’ve tried so I thought I would make these and then see if I needed to change anything to add that extra flavor. They were very good on their own but I liked them better with more cinnamon added in. I kept mine in the fridge because I thought they tasted better cold than room temperature. Super moist and delicious! Highly recommend!
Shelley ohanesian
0In love with this recipe, I chose the butter option, my first bite was heavenly buttery with salted publishers on top… Ohhh yessss
Willadean Milam
0I read all the wonderful reviews and my muffins just did not come out like everyone else. I wonder if it was the amount of baking powder a tablespoon seemed like a lot and if it not being gluten-free would make a difference. I want to try the recipe again so please tell me what I could do to make them moist and delicious.
Thank You
Wholesome Yum M
0Hi Willadean, If your muffins were flat all through the baking process, then it may be due to expired baking powder. If they rose in the oven and then fell when they were taken out to cool, then they weren’t fully baked and needed more time.
Erin
0I was dx’d with Diabetes T2, 2 months ago and don’t like any of the sugar subs I have tried. I love Fall and was sad I wouldn’t be able to partake in the Pumpkin everything and then ran across this recipe. With a heavy heart, I decided one more try and bought the ingredients. At the very least I could bring them to work and leave them in the breakroom… I made them today and there is no aftertaste! They are moist and delicious! WOOT!! I added less sweetener than called for and threw in a tablespoon and a half of dark choc mini chips. Thank you so much for sharing this and the video was an added bonus! I’m currently perusing the other recipes and can’t wait to try them all!
Erika
0These satisfied my all-things-pumpkin-spice FOMO! The flavor, texture, and moistness is perfect. I melted Kerrygold salted butter for the oil. The muffins baked up beautifully in 25 min. and no issues with over-browning.
Pam Kirsch
0These pumpkin muffins are absolutely delicious!! They are so moist and flavorful! I had 2 right out of the oven with butter – yum. Tomorrow I’m going to make some pecan or walnut cream cheese spread to put on them – can’t wait. Thanks for another fabulous recipe!
Nicola
0Made this recipe tonight and it turned out AMAZING!! I also added some cream cheese mixed with erythritol into the centre of each muffin and o m g it was soooo good. Thanks for the fab recipe – will defo be making again 🙂
Sandra
0I have tried many of your recipes but today i made these and mixed up a basic cream cheese icing and I thought I went to heaven. Absolutely loved it!!! Second only to your famous cheesecake recipe. Thank you!!
Linda Sanders
0Love these muffins. I made them this week for a team lunch and they were a hit!
Laura
0These pumpkin cupcakes are awesome!!! So moist, tender, packed with flavor. I put sliced almonds on top. They’re a big hit everywhere I take them!! Nobody can believe they’re low carb!!! Thanks so much for this recipe. I’ve made other recipes on your site and they’re all sooooo good!! Thanks so much.
Kim
0These sound fantastic!! I need egg free. Have you ever done flax eggs or chia eggs?
Wholesome Yum M
0Hi Kim, Other readers have had success making these with flax eggs. It was noted that they may need to bake longer than the listed time in the recipe. Enjoy!
Kayla Mcintyre
0Hi I’ve been trying to find a recipe with just almond flour and couldn’t!! I don’t use coconut flour, and was wondering if I can just use almond flour? Thank you. I’ve been dying to try this recipe
Wholesome Yum A
0Hi Kayla, the coconut flour is necessary in this recipe to absorb moisture from the pumpkin. You might have better luck modifying this recipe to include pumpkin pie spice and pumpkin seeds instead of blueberries.
Karen Shaw
0If I were to add a non-keto sweetener, e.g. maple syrup, brown sugar, or honey, do you know how much I should use in this recipe? Thanks!
Wholesome Yum A
0Hi Karen, I don’t work with those sweeteners much so I’m not sure. Be aware that substituting granulated sweeteners with liquid ones may also change the final texture.
Natalie
0Had these muffins at a friend’s & asked for the recipe because they’re soo good! I added 60% cacao chips too. I used monkfruit sweetener. They came out really well & I cant wait to try your other recipes. I’ve been reducing my carb intake recently-paying attention to the numbers. This treat really helps me to not “lose it” -meaning to keep me from falling off the low carb wagon! Thanks for your research & sharing your recipes! Thank you?
Tonia
0I’ve been exploring options for my 4 year old, who was recently diagnosed with Type 1 diabetes & is the pickiest eater alive! I have tried sooo many recipes but this is the only thing he’s actually liked (& eaten)! I can’t tell you what it means to have even one healthy option for him as his blood sugar levels are a constant battle. I look forward to trying more of your recipes!
Sierra
0Hi! I’m a huge fan of your pumpkin bread recipe and thought I would use this one for muffins! However, it calls for 1 tbsp of baking powder, which is almost double what your bread recipe uses.. could this be a typo? I made the recipe last night and am noticing that the taste seems off.
Wholesome Yum M
0Hi Sierra, Thanks for checking! The amount of baking powder listed is correct.
Peg
0All I can say is, “WOW!” These were absolutely amazing! They were fluffy, flavorful and such a great treat for a lazy Saturday. I substituted xylitol for the sweetener, which did add a few carbs but I’m a little burned out on the taste of Swerve. I also topped the muffins with walnuts instead of pumpkin seeds and used butter instead of ghee. The batter was very thick and required 32 minutes total baking time, but the end product was truly amazing. Thanks for letting me have a little treat without blowing my low carb eating plan!
Nineveh
0Wonderful! Thank you for sharing! I added a teaspoon of cream cheese to each muffin before putting in the oven.
Brenda
0Hi made the recipe first just as it was and the second batch used only almond flour , no coconut flour and I used olive oil instead of coconut oil and the second batch are as good as first even slightly better . I live in high altitude area sometimes I mix it up!
Sallie
0Are you sure this is gluten free? I’ve developed a gluten allergy after learning about gluten. Also, what’s keto? Would love to see more about it on your blog
Maya | Wholesome Yum
0Hi Sallie, Yes, these are definitely gluten-free. You can learn more about keto here.