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- Besti Monk Fruit Allulose Blend – I originally made these almond flour pumpkin muffins with erythritol sweetener, but updated the recipe to use Besti instead, because it makes them more moist and gives them a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
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.
Madison
0Loved this. I Doubled the recipe, so I could use the whole can of pumpkin. And I added mini chocolate chips to the batter. Turned out great. Very moist and flavorful!
Pamela Bakka
0I have a similar recipe for gluten free pumpkin muffins which contains 6 eggs instead of for coconut flour and coconut oil along with the spices- I also add a cup of chopped walnuts it makes 12 Muffins and they are absolutely delicious! Just wish I knew how much protein was in them since I’m not drinking protein powder anymore…
Susan Stroud
0Wow! These are really yummy. I haven’t had much luck with low carb baked goods but these are good enough to share with friends who aren’t low carb
France
0I Just made these, double recipe. OMG delicious… it is very hard to stop at one… thank you for sharing… this will be breakfast, snack, dessert…
Nita
0I absolutely love your Keto pumpkin muffin recipe. I’ve made it twice now. It satisfies my craving for something with bread like consistency. It is also very quick and easy to put together. I made two little changes as I had monk fruit sweetener in a bag, which is really only part monk fruit but known to be very very sweet. I used half the amount listed for sweetener. I also just sprayed my muffin pan the second time and put the muffin mix straight in the pan with no paper cups. They just pop right out after cooling for a few minutes. The first batch in paper cups left too much of that good muffin stuck to the paper.
They are a delightfully moist treat, warmed up for 20 seconds in the microwave, to have with coffee or for dessert after dinner, with tea.
Vickie M
0Hubby and I have been trying to find more coconut flour dessert recipes so when I saw this we decided to give it a try. I had never tried one that used the same amounts of both almond and coconut flours but I’m sure glad I tried this one….we just love them! They will definitely be made again and again…our new favorite. I also love just using one bowl and a spoon to mix it all up. I used a small cookie scoop (used 2 scoops each) and made 12 muffins…maybe my muffin pans are smaller. I pressed chopped walnuts into the tops of mine…yummy! Thank you so much for this recipe.
lisa
0Oh wow I love this recipe! I substituted mashed ripe bananas for the pumpkin puree and added blueberries at the end. I also used monkfruit sweetener. They came out perfectly! They are absolutely delicious! Thank you for the recipe!
Cheryl
0Made these yesterday. Good warm, even better next day. I automatically cut the sweetener and add pumpkin (recipe I saved called for less) — came out perfect anyway. Froze a few. Texture is perfect. Cheryl
Nita OBrien
0They looked so yummy, we split one that was still warm. Oh my, these are just so deliciousness. Thank you. The only change I made was to use half the sugar, (monk fruit sweetner)
Kathy
0I just realized that I’m out of butter and wondered if olive oil will work. If so, would the measurement be the same?
Michele
0I use coconut oil with the same measurement and I prefer it to the butter . I use silicone muffin molds and they slide right out. I absolutely love these muffins and try to always have some in the freezer.
Maya | Wholesome Yum
0Hi Kathy, It might work, but the texture and flavor would be different. If you have coconut oil, that’s a more similar substitute.
Kathy
0When I calculated the recipe using the My Fitness App, the nutritional value came up as 177cal, 4.1 carbs, 12.1 fiber (no idea how that could happen) 14.1 fat and 9.1 protein. It’s very similar to your calculations except for the protein and fiber. Any thoughts on this?
Maya | Wholesome Yum
0Hi Kathy, It will depend on the ingredients selected and unfortunately I can’t troubleshoot 3rd party apps. The nutrition info on this site comes from the USDA Food Database which is most accurate.
Ann Bodmer
0I just made these muffins and they were DELICIOUS!!! I will add nuts cranberries next time. I also shared your recipe with my KETO friends. Thanks for sharing your wonderful recipes. Merry Christmas and Happy New Year!!!
Courtney Adkins
0These are SOOOOOO good! They have become a staple in our house…breakfast, snack, dessert…these muffins do it all! Thank you for such an amazing recipe…love that they use both coconut and almond flour and you can make them pretty much dairy free!
Kathleen Kett
0The best keto muffin recipe ever. I’m wondering whether you can substitute full fat sour cream for the pumpkin purée and make blueberry lemon muffins—just for another variation but I don’t want to ruin a good thing.
Maya | Wholesome Yum
0Hi Kathleen, Possibly – I haven’t tried that. I have a popular recipe for keto blueberry muffins here that you can try, but it doesn’t use sour cream.
Kathy Bushey
0Just made the pumpkin muffins. They were very easy to make and are delicious. Thanks so much.
Cora
0These are great muffins! Thanks for providing this recipe. They are moist, taste great, low in carbs (I’m doing keto), filling and filled that spot for something bread like for my breakfast.
Anna
0We made these Thanksgiving Day because I wanted something with pumpkin. I left out the sweetener because we don’t like the taste of it and I’m trying to not use any in my Keto diet. Maybe because I’ve become used to non-sweet things that they tasted soooo yummy! With the pumpkin pie spice, pumpkins, and vanilla, it was enough. Smothered in Kerrygold butter and I was in heaven. So satisfying with my eggs in the morning. Thank you so much, I don’t think I’ve ever gone wrong with one of your recipes!