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- Besti Monk Fruit Allulose Blend – I originally made these almond flour pumpkin muffins with erythritol sweetener, but updated the recipe to use Besti instead, because it makes them more moist and gives them a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
Kaysha
0Thank you so much for this recipe! This was the second recipe I’ve tried and I enjoyed it so much. I used swerve sweetener. Mine burnt on the tops because I was distracted, but were still moist in the middle which was a surprise! Today (Day 2) I sliced one in half and toasted it and smeared some cream cheese on each “slice”. I was blown away! I think I’ll try to use less sweetener in future batches so they can be used with other spreads and have less of the cooling effect the swerve sweetener gives!
Marissa
0These are amazing! Very easy to make. I used granular Swerve and vegan butter (I’m not vegan so eggs are fine, but dairy allergy) and these are perfection. Thank you for a wonderful recipe.
Yvonne L Bailey
0Amazing recipe! Used monk fruit and had no aftertaste. Also used coconut oil that was in liquid form. They were very moist and tasted great . Added pecan pieces on top. 25 minutes in the oven at 350 was perfect. They looked like ones from a local bakery. My new favorite Keto recipe! Wish I could share a pic.
Wholesome Yum M
0Hi Yvonne, I’m thrilled you loved these muffins! You are welcome to share images in the Facebook group!
Lindsay
0WOW!!! I can’t believe how moist and flavourful these are. They remind me of a muffin you’d get during PSL season at a local Starbucks but WITHOUT the added sugar. Love, love, love! Will definitely make again.
Danielle
0I just made these and they are perfect! Done in exactly 25 minutes. Amazingly moist, perfect texture! I added 1/2 tsp more vanilla, a smidge more spices and used 1/4c classic & 1/4c golden monk fruit. I really needed this today & had a pat of butter and hot cup of coffee ready before they were out of the oven and had one immediately! Somehow I got 12 so I’m hoping to have a few left to freeze! Thank you so much for this recipe & for all of your other recipes! As someone who only sometimes loves cooking, I really appreciate the simplicity of your recipes! Thank you!
Richard Levy
0Fantastic! Easy to make and delicious. I used coconut oil and Monkfruit sugar and they came out great. I sprinkled a little extra Monkfruit on the tops when I took them out of the oven and it tasted like a crumb topping.
Julie
0Great recipe! Used my own spice mix though. Pregnant daughter loves these so I’m making a batch every week!
Bridget L.
0These muffins are delicious! My non-keto mother and husband both loved them!
Linda
0I made these muffins for the first time this morning using butter and Splenda. The flavor was awesome and they seemed moist enough however they didn’t want to hang together. They crumbled at the lightest touch which I found surprising since they had four eggs. Any suggestions?
Wholesome Yum M
0Hi Linda, These muffins should not be crumbly. Did you make any other substitutions?
Linda
0Nope, no other substitutions.
Wholesome Yum M
0Hi Linda, In that case, I would consider adding a little oil. 1-2 tablespoons of melted coconut oil should help with crumbling.
Kate
0This recipe was absolutely fabulous. Simple one bowl recipe. I cut the sweetener to a bit over 1/2c and would be happy with less too (used trim healthy mama xylitol/erythritol/stevia powder mix). Texture was spot on. Flavour amazing.
They browned nicely, and I used my new Trudeau Structure silicone muffin pans without liners. The muffins slipped right out and browned nicely on top and sides. No greasing of the pans necessary at all.
10/10 in my books, will for sure be making them again. I really LOVE the coconut/almond flour combo and hope to make more similar muffins in the future.
Zoe Horvath
0Nice and easy recipe! I used about 1/3 cup of erythritol and would probably go with 1/4 cup next time. Otherwise, really yummy!
Glenda Seal
0I have made this recipe many times using almond flour and it always turns out great. Everyone enjoys them. I didn’t have any almond flour so tried making them using golden flaxseed meal. There were still delicious even with a grainier texture. So far all the recipes I have tried have been great.
Jana Razo
0Wow these were amazing! An my toddler loved them too. Thank you for the recipe. I’ll be making these a lot!
Katie
0I LOVE all of your recipes! I bought the cookbook and am also LOVING that as well! My favorite recipes (so far!) from your cookbook are the pecan salmon (so yummy!) and the quiche lorraine! Those are in our dinner rotation regularly! One question about this recipe- would you recommend using granulated or confectioners Swerve? I didn’t realize that (at least I think??) they do not substitute exactly one for one. I believe that using the granulated version would be using about twice as much as the confectioners??? Anyways, just wondering which type you created the recipe with so it comes out as you intended! Can’t wait to make these for Thanksgiving week’s breakfast!
Wholesome Yum M
0Hi Katie, This recipe uses granulated erythritol or allulose. The powdered vs. granulated sweeteners are roughly the same “sweetness.” The difference is most notable in the final texture of the recipe, which is why the recipes on Wholesome Yum use both types of sweeteners. Enjoy!
Juli
0I love these muffins! They are dense and very moist. They were still a bit difficult to remove with my silicone muffin pan, so next time I will spray it first. Fill to the top as recipe states, they do not rise.
Modifications:
I only used HALF the monkfruit sweenener (1/3 cup) and they were plenty sweet. I added a sprinkle of cinnamon/monkfurit on top.
I used avocado oil instead of ghee.
Nicole S
0My daughter made these last night, they are so good! We used coconut oil and added more spices bc we love flavor. We will be making these again soon, probably when she wakes up. lol I had one for breakfast this morning and even better today. Thanks for the yummy recipe!!
Andrea
0So good!!! I used less than 1/2 cup or Erythritol and they were still plenty sweet!! I got about 11 muffins out of this recipe.
Carol
0Just made these wonderful muffins. I have been trying to stay on a low carb diet to help my blood sugar. I am not normally a sweets person, but fall is tough with all the pumpkins stuff. These are delicious. I did use only a half cup of the sweetener and that was fine for me. So moist and flavorful. After canning 14 quarts of pumpkin yesterday and having a some left over I really needed something pumpkiny. These absolutely hit the spot.And so easy to make.
BrendaW
0These were awesome! Super moist and full of flavor! Used a cream cheese frosting on top! My daughter loved them!
Linda
0These muffins are fabulous! I make them for my work peeps and they just love them!
Jodi Bachor
0Hi. I made these today but something went wrong. I think it’s that the recipe I was following called for 1 table spoon of both Pumpkin pie spice and Baking powder. I’m thinking those should be teaspoons? I double checked and the recipe definitely says tbsp
Maya | Wholesome Yum
0Hi Jodi, I’d love to help but hard to tell without more info – what went wrong for you? The amounts on the recipe card are correct.