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- Besti Monk Fruit Allulose Blend – I originally made these almond flour pumpkin muffins with erythritol sweetener, but updated the recipe to use Besti instead, because it makes them more moist and gives them a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
Ann Turner
4Very tasty but a few thoughts: The ratio of liquid ingredients to dry is off. I would leave out one egg and increase almond flour by 1/2. I had to cook these for 37 min. to get them firm.
Sharon Leslie
2Decadent! Made with monk fruit/erythritol blend. Topped with chopped walnuts. Made 10 jumbo muffins. Could make 11 rounded tops in my pan. Thanks for the recipe!
Carol
1This is the best pumpkin muffin recipe I have EVER made! It’s moist and fluffy and everything you could want in a pumpkin treat. I did not have pumpkin seeds available, so I topped with chopped pecans. I used my own chicken eggs, so I increased by one egg because they are still laying small eggs.
Maya | Wholesome Yum
0Thank you so much, Carol! Chopped pecans sound perfect.
Brenda
1Made these yesterday and they are so moist and delicious! My husband loved them too. Will definitely be making them again soon! Thank you Maya!!!
Maya | Wholesome Yum
0Thank you, Brenda! I’m so happy you and your husband enjoyed them.
Kristyn
1These are amazing!! They have the right amount of pumpkin flavor & are so soft! You have the best keto recipes!
Susan
0Should the almond flour be packed or loose?
Maya | Wholesome Yum
0Hi Susan, It should be loose, either scoop or spoon the flour into the measuring cup and then level. Hope this helps.
Laurie
0Hello, new favourite muffin recipe! These came so good, moist with a lot of flavour!
I didn’t have Wholesome Yum brand flours (I do have the sweeteners, though!) but Bob’s Red Mill has never let me down. I also didn’t have “pumpkin pie spice” but found that I DID have all of the components that typically make pumpkin pie spice – cinnamon, nutmeg, cloves, ginger – which I just eyeballed while mixing the dry ingredients. I also decided to use the Besti brown sugar substitute in lieu of the granulated white substitute, in the hopes that it would yield a slightly richer sweetness (I… think it did? Certainly didn’t hurt it!)
For the topping I sprinkled on a blend of nuts and seeds (including pumpkin seeds) from a keto trail mix. The end result was an incredibly soft muffin with a little bit of crunch on top.
I did have to give them another 5 minutes baking time, as they did not pass “the toothpick test” with the initial 25.
Ultimately they earned positive reviews from the family, even my picky Italian mother, and I plan to add this recipe to my regular baking rotation!
Wholesome Yum D
0Laurie, this is the kind of review I love reading! Your spice blend sounds spot on, and using the Besti Brown for a richer flavor was such a great call. And that nut and seed topping? Perfect for a little crunch.
Jules
0I LOVE LOVE LOVE THESE!!! I was looking for a pumpkin recipe and these are amazing and SOOO MOIST!!!! I absolutely will be making these again!!!!
Wholesome Yum D
1I love your excitement, Jules! So glad you found the perfect pumpkin treat and yes, that moisture level is everything. Thanks for sharing!
Jules F
0These were soooo delicious!!! I made the keto pumpkin bread first but overcooked them accidentally so I made these and kept checking the time! They are moist and fluffy! I made them in a mini loaf pan (6) and they are perfect!!!
Wholesome Yum D
1I’m so glad these turned out perfect for you, Jules! Mini loaves sound like such a fun way to enjoy them. Great save after the first batch, sounds like round two was a big win!
SUSAN
0These muffins are INSANE!!!! I topped them with chopped walnuts. I found this batter fully filled 12 regular sized muffin cups, not 10. I will make these forever!
Wholesome Yum D
0I love that, Susan!! So glad you’re obsessed with the muffins, chopped walnuts on top sound amazing. Thanks for sharing!
Sandy M
0I love these! I made them for Thanksgiving brunch today and no one missed pie. Yum!
Wholesome Yum D
0I’m so glad to hear that, Sandy! What a fun idea for Thanksgiving brunch, I love that they were a hit even without pie. Yum is right!
Leslie
0Made the muffins for my husband and I, strictly by the recipe. Perfect!
Wholesome Yum D
0Thanks for the kind words, Leslie! So happy they turned out perfect for you and your husband, love when that happens!
Jules
0I’m curious to know if anyone has made this and the keto pumpkin bread and can help me decide which to make – most of the same ingredients but would love to know if anyone has any suggestions or thoughts on which one is better than the other for a November treat…
Maya | Wholesome Yum
0Hi Jules, I think both are great! I think it mostly depends on what format you prefer, a bread or a muffin. Please let me know which you go with and how you like it!
John
0I’ve made these a few times, also made with apple sauce. They’re moist and delicious.
Wholesome Yum D
0Appreciate you sharing that, John! Sounds like a delicious twist with the applesauce.
Linda Engstrom
0I made these this morning. I added 2 tbsp brown Truvia and used butter. For the 1/2 cup milk I used 2 tbsp heavy cream and the rest water. I put 50 pecan halves and 1 tsp butter with 3 tbsp brown Truvia and allulose in a small frying pan until dissolved and syrupy and topped the muffins with this. They were absolutely perfect, moist and delectable. Hubby commented, you’re sure these are Keto? Winner winner!
Wholesome Yum D
0That topping sounds incredible, Linda! I love how you made it syrupy with pecans, what a perfect touch. And your husband’s reaction is the best compliment! So glad these were a winner for you both!
Tammy M Marsh
0I agree with reviewers that the other half cup of almond flour for structure would be beneficial. This is a delicious recipe. Taste just like pumpkin pie as is with some whipped cream is yummy.
Donna Nordman
0These muffins are a 10 in my book!! I sifted all the dry ingredients in my food processor to get any clumps out and get things mixed up well, dumped them out in a large bowl then added the wet ingredients. I didn’t have the monk fruit blend in your recipe so I used half powdered allulose and half Swerve brown. I actually got 12 regular sized muffins from this recipe, and they taste fabulous with your cream cheese frosting. Thank you, Maya!!!
Wholesome Yum D
0I’m so happy to hear that, Donna! Your tweaks sound perfect and I love that you paired them with the cream cheese frosting. So glad they were a 10 in your book!
Tonya Kilpatrick
0Can you substitute the sweetener with half honey and half sugar substitute?
Maya | Wholesome Yum
0Hi Tonya, Sorry, I don’t recommend doing that because the wet/dry ratio will be different. The batter will likely be too runny and the muffins won’t set. But let me know how it goes if you try it.
Michele Cammarata
0Hi! I added a TBS of Instant Coffee and a 1/ 2 each chopped pecans and Lily’s Dark Chocolate Baking Chips. Decadent, delicious Muffins! Thank you for the recipe.
Maya | Wholesome Yum
0I’m so glad you liked these, Michele! Thank you for sharing your variation.
Fred
0These are decent per recipe. I’ve made them 5 or 6 times now and each time small changes have been introduced, as I find the original recipe a little light on flavor. I add 2.5 tablespoons pumpkin spice, which may seem extreme, but that’s where I landed. I also definitely recommend the pumpkin seeds. Last, I top them with a small amount of a cream cheese frosting (cream cheese, vanilla, allulose). That’s a lot of tweaks, and I apologize for that, but it’s my honest opinion what’s needed to keep me coming back to them.
Maya | Wholesome Yum
0Thanks for sharing your variations, Fred! I do like these with sugar-free cream cheese frosting too — it makes them feel like a cupcake.