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- Besti Monk Fruit Allulose Blend – I originally made these almond flour pumpkin muffins with erythritol sweetener, but updated the recipe to use Besti instead, because it makes them more moist and gives them a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.
FREE 5-Ingredient Recipe EBook

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.
-
Preheat the oven to 350 degrees F (177 degrees C). Line 10 muffin cups with parchment liners (I use this muffin tin).
-
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.
-
Stir in the the eggs, pumpkin puree, almond milk, melted ghee, and vanilla, until completely incorporated.
-
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.
-
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.
Add Your Notes Your Notes
© Copyright Maya Krampf for Wholesome Yum. Please DO NOT SCREENSHOT OR COPY/PASTE recipes to social media or websites. We’d LOVE for you to share a link with photo instead.
Almond Flour Pumpkin Muffins

Shop
My
Custom












391 Comments
Nicole
0These came out amazing! I wanted something that felt like fall and this hit the spot! I added a dollop of keto friendly cheesecake better to the top before baking to make these pumpkin cheesecake muffins. This increased my servings to 16 cupcake sized muffins. So still very low carb.
Cara
0Where have these been all my life??? I don’t have (and have never cooked with) Erythritol so I used about 1/4c of maple syrup to add some sweetness. I added a few pecans on top and I substituted 1/2 of the ghee with raw cacao butter and it is AMAZING!!! The cacao butter gives a hint of chocolate, and I love chocolate and pumpkin together. The consistency of these is perfect with the blend of almond and coconut flours.
THANK YOU for such a great recipe!!! ❤️
Maya | Wholesome Yum
0Thank you for sharing, Cara! That cacao butter substitution sounds delicious.
Wendy
0These are absolutely delicious! My sweetener of choice is Monkfruit sweetener that is blended with erythritol. I actually had less on hand than I thought and intended to augment with liquid Stevia but after adding the monkfruit sweetener, I tasted and it was just sweet enough. This was about 1/3 cup, maybe a little more. I’ve been keto since March 2018 so it doesn’t take much for me to taste “sweet”. Point of the story is maybe taste-test after half the sweetener. I LOVE the texture. So moist! Thank you!
Maya | Wholesome Yum
0I am so happy to hear that, Wendy! Thank you for stopping by!
Doreen
0Hi!
Can I make this recipe in a pyrex loaf pan?
Thank you!
Maya | Wholesome Yum
0Hi Doreen, Yes, you can. The baking time would be a lot longer. You can also try this low carb pumpkin bread recipe.
Elaine
0I love these muffins! I added half a cup of pecans. And next time, I will, also, add a half cup of whole fresh or frozen cranberries.
Maya | Wholesome Yum
0I am so happy you liked them, Elaine! Have a great day!
Lisa
0Fab recipe! Made them twice in a week. I used Truvia and used the conversion factor provided in your link. I only added 2 tablespoons of Truvia rather than the 3.5 recommended as dont like things overly sweet and they were perfect. Great for lunches/travelling and nice with cream cheese.
Thanks
Maya | Wholesome Yum
0I am so happy you liked the muffins, Lisa! Please come back soon!
Lori Daly
0Hi Maya,
I made the Keto Pumpkin Muffins and they are delicious! So moist and even a little fluffy. Thank you for creating this recipe!
Maya | Wholesome Yum
0I am so happy you liked it, Lori! Thank you so much!
Barb Vinton
0Thank you so much- Bought some cashew and pistachio nutty butters – what a heavenly marriage of flavor…
Maya | Wholesome Yum
0Love that, Barb!
Michele
0Thank you for this recipe. Made a batch this morning and added a few pieces of pecans. They were delicious. I will be adding these to my other “excellent” recipes. Happy holidays!!!
Maya | Wholesome Yum
0I am so happy you liked the muffins, Michele! Thank you!
Christine Blanksvard
0Cooked these last night. With my family eating keto and my Mom a type one diabetic they were the perfect solution to our pumpkin cravings. Easy to follow recipe with great pictures. They came out moist and yummy! Going to try using creme cheese in them next! Thank you!
Maya | Wholesome Yum
0I am so happy to hear that, Christine! Thank you!
Judy
0Hi, Just saying but I used MCT oil, and also added 2 T Manuka Honey…they turned out great!
Maya | Wholesome Yum
0Thanks for sharing with us, Judy! I am glad you liked them!
Donna Curson
0I just made your pumpkin muffins and they are awesome. I used 1/3 cup Triva and butter. Also used my own spices , they are so very good. I’m Diabetic so this is great and low carb and sugarless. Thank you so much. Donna Curson
Maya | Wholesome Yum
0I am so happy to hear that, Donna! Thank you!
Christine Blanksvard
0I would like to add a cream cheese center, any suggestions? Thank you so much for all your reciepes.
Maya | Wholesome Yum
0Hi Christine, I haven’t tried that, it sounds delicious! You could probably beat cream cheese with a sweetener and vanilla, then push large pieces of that into the center of each muffin before baking. Let me know if that works!
Shirley A Phillips
0Do you have other recipes so I can use more of the coconut flour? Got a 4 pound bag.
Maya | Wholesome Yum
0Hi Shirley, Yes, I have lots of other recipes with coconut flour – just use the search box.
Shirley A phillips
0Loved the pumpkin muffins and made some changes.
Used 1/4 c butter and 1/4 c applesauce.
Used 1 c stevia.
Did not use cupcake papers. Merely sprayed my nonstick pan and they came out perfectly!
Maya | Wholesome Yum
0Thanks for sharing with us, Shirley!
Jaime Johnson
0LOVVVVVVVE the pumpkin muffins!! Would doubling this recipe affect anything?
Maya | Wholesome Yum
0Thank you so much, Jaime! You can definitely double it. 🙂
Carrie
0These turned out delicious. Thank you for yummy recipe.
Maya | Wholesome Yum
0I am so happy to hear that, Carrie! Thank you!
Jeanette
0Just made these muffins and they are wonderful! A nice fall treat.
Maya | Wholesome Yum
0I am so happy you liked the muffins, Jeanette! Have a great day!
Debra W
0I made these this morning for my women’s Bible study group. I made them mini without liners and they came out great. Instead of using erythrotol I used Monk fruit sugar and coconut sugar. I sprinkled a little Monk fruit sugar on top as well. Even the non-healthy peeps enjoyed them!
Maya | Wholesome Yum
0I’m so glad to hear that, Brenda! Have a great day!
Calbeauty1
0Made these last night and they we’re soooo good!!! Had my dinner guests try them too….who aren’t on a keto diet….and they we’re surprised how good they tasted. Bravo!!
Maya | Wholesome Yum
0I am so happy you liked the muffins! Have a great day!