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Free Printable: Low Carb & Keto Food List
Get It NowLow carb pumpkin recipes are one of the best things about fall! Especially healthy, low carb keto pumpkin muffins. These are deceptively simple, but taste so rich and cozy — most people won’t believe they’re coconut and almond flour pumpkin muffins! They’re made with real food ingredients and no sugar whatsoever… and taste perfect with a hot cup of keto butter coffee for a satisfying breakfast.
If you love pumpkin recipes this time of year, be sure to also try pumpkin pie cupcakes and keto pumpkin roll.
Which flour is the best one to use for healthy pumpkin muffins? Naturally, as with all my keto desserts, I only considered low carb flours. I experimented on keto pumpkin muffins with almond flour, coconut flour, and flax seed meal. Almond flour alone can be too heavy, coconut flour is too dense, and flax seed meal can be a little gritty. In the end, I settled on a combination of almond flour and coconut flour.
Making the low carb pumpkin muffins with coconut flour and almond flour helps create the best texture, better than one or the other alone. The coconut flour also helps keep them lighter. Low carb coconut flour recipes tend to be less heavy than almond flour ones.
In particular, I use a blend of Wholesome Yum Almond Flour, Coconut Flour, and Besti Monk Fruit Allulose Blend for the batter — the allulose keeps them super soft and moist, while the mix of flours keeps them cake-like. They make the ultimate pumpkin keto muffins that anyone can enjoy, whether or not they’re keeping track of carbs.
Why You’ll Love This Low Carb Keto Pumpkin Muffins Recipe
- Rich pumpkin spice flavors
- Moist, cakey texture
- Uses basic keto baking ingredients
- Just 10 minutes prep time
- About 4 grams net carbs per muffin
Almond Flour Pumpkin Muffins Ingredients
This section explains how to choose the best ingredients for keto pumpkin spice muffins, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.
- Wholesome Yum Almond Flour – This flour creates naturally gluten free pumpkin muffins, and it’s finely milled for a more authentic texture.
- Wholesome Yum Coconut Flour – This flour is made from one ingredient (pure organic coconuts!) and helps absorb the extra moisture from the pumpkin. Don’t skip it!
- Besti Monk Fruit Allulose Blend – This sweetener helps the muffins bake up soft, all with 0g net carbs. You may be able to substitute erythritol or another sugar replacement here (use the sweetener conversion chart), but the taste and texture will be different.
- Baking Powder
- Pumpkin Pie Spice – This is a blend of spices, including ground cinnamon, ginger, nutmeg, cloves, and allspice. You can get it pre-mixed or make homemade pumpkin pie spice instead.
- Sea Salt
- Eggs – Use whole, large eggs.
- Pumpkin Puree – You can make your own or get it canned. Avoid getting canned pumpkin pie filling, which contains added sugar.
- Almond Milk – Either plain or vanilla is fine, but make sure it’s unsweetened. You can order it online, get it at the grocery store, or make homemade almond milk. Other types of keto friendly milk would also work fine here.
- Ghee – Ghee makes these paleo pumpkin muffins, but you can also use butter or coconut oil instead. I admit I usually use butter when I make these.
- Vanilla Extract
- Pumpkin Seeds – These are pepitas, the hull-less seeds from specific varieties of pumpkins. Avoid seeds with the hull, which can be tough to chew in this recipe. You could easily swap these with walnuts, pecans, or sugar free chocolate chips, or top with a layer of cream cheese frosting after baking.
See the variations section below if you want to make these nut-free, dairy-free, paleo, or with cream cheese filling.
How To Make Low Carb Almond Flour Pumpkin Muffins
This section shows how to make keto friendly pumpkin muffins with step-by-step photos and details about the technique, to help you visualize it. For full instructions, including amounts and temperatures, see the recipe card below.
- Mix dry ingredients. In a large mixing bowl, combine flours, sweetener, baking powder, pumpkin pie spice, and sea salt. Whisk well to ensure no clumps.
- Add wet ingredients. Add eggs, pumpkin puree, almond milk (or keto milk of choice), ghee (or fat of choice), and vanilla. Mix until completely incorporated. (It will be thicker than a traditional muffin batter — this is normal.)
- Scoop. Spoon the batter into a muffin tin lined with paper liners. Smooth the tops and sprinkle with pepitas.
- Bake. Bake in a 350 degree F oven until golden and an inserted toothpick comes out clean.
Tips For The Best Low Carb Pumpkin Muffins
Making keto pumpkin muffins with almond flour and coconut flour looks a little different than using traditional white flour, so keep these tips in mind.
- Choose the right fat. Go with ghee, butter, or solid coconut oil (melted). Avoid fats that are liquid at room temperature (i.e. olive or avocado oil), since the muffins will take on a different texture.
- Expect a thick batter. These keto pumpkin muffins need a thicker batter than most muffin recipes, even low carb muffin recipes. (For example, low carb keto blueberry muffins have a thinner batter.) But, because of the way the pumpkin and coconut flour interact with each other, this one starts out thicker. Don’t worry, the muffins won’t be dry!
- Fill muffin liners close to the top. Almond flour and coconut flour don’t rise as much as wheat flour, so the muffin liners should be pretty full. If you only fill them 1/2 or 3/4 of the way, you won’t get much of the best part – the muffin tops!
- Ensure doneness. An inserted toothpick should come out clean. Underbaking the muffins can cause them to fall (deflate) or be too wet inside. If muffins are browning too quickly, you can tent the pan with foil until they’re done.
- Cool if possible. This is not required, but cooling improves the inner texture. I do usually reheat them in the microwave or the oven when ready to eat. Adding a pat of butter to a warm muffin is just perfect!
Variations
One of my favorite things about this low carb pumpkin muffin recipe is that it’s easy to customize to make additions or fit any dietary restrictions. Below are the most common ones people ask me for.
Nut-free variation:
- Sub the almond flour: When I first published this low carb pumpkin muffins recipe, I said that golden flaxseed meal is a great almond flour replacement if you are nut-free due to allergies, or need to send these muffins to a nut-free school with your kid. However, I have since revised my recommendation and much prefer sunflower seed meal instead. It is also nut-free, but creates a much better texture than the flaxseed meal. That being said, almond flour still makes the best keto pumpkin muffins in terms of texture and flavor.
- Sub the almond milk: Replace it with coconut milk beverage — the liquid kind in the dairy section, not the thick kind in a can.
Dairy-free or paleo variation:
Although I make lots of paleo recipes, I wasn’t really planning to make paleo pumpkin muffins in this case. Fortunately, I was pleased that they turned out that way. Virtually all the ingredients are already paleo friendly!
- For the sweetener: Allulose is a natural sweetener, but some people prefer not to use it while following a paleo lifestyle. If that’s you, no problem. You can easily use another granulated sweetener in your paleo pumpkin muffins, like coconut sugar. That would not be sugar-free, but is natural and paleo friendly.
- For the fat: This recipe uses ghee as the fat, which is often okay for most dairy sensitivities, but coconut oil works fine if you need to be more strict. I personally am not dairy-free, so I often use butter. Both ghee and coconut oil would be paleo friendly as well.
If your version of healthy pumpkin muffins needs to be vegan, that’s not really my thing so I highly recommend these vegan pumpkin muffins instead. She has a gluten-free variation, and you can swap the sugars with sugar-free sweeteners if you’d like.
Keto Pumpkin Cream Cheese Muffins:
These almond flour pumpkin muffins go perfectly with the cream cheese filling I made for my keto cinnamon cream cheese muffins recipe. Simply follow the recipe below to make the batter, then click the link for instructions on assembling with the cream cheese filling. (You’ll get a few extra muffins if you add filling, compared to the ones without filling.)
Storage Instructions
- Store: Store this keto pumpkin spice muffin recipe in a covered container on the counter for 2-3 days, or in the refrigerator for up to one week.
- Freeze: Store in a freezer-safe container. Thaw at room temperature before serving.
More Low Carb Pumpkin Recipes
If you like keto coconut flour pumpkin muffins, you’ll love these other low carb ways you can use pumpkin:
Tools To Make Pumpkin Keto Muffins
- Muffin Pan – Has enough wells for a full batch of muffins!
- Paper Liners – The perfect nonstick liners that release clean.
- Silicone Liners – A reusable (and colorful!) liner option.
Almond Flour Keto Pumpkin Muffins Recipe
Low Carb Keto Pumpkin Muffins Recipe
Bake up low carb keto pumpkin muffins so rich and moist, you won't believe they have 4g net carbs each! And, these almond flour pumpkin muffins are ready in 35 minutes.
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Ingredients
Tap underlined ingredients to see where to get them. Please turn Safari reader mode OFF to view ingredients.
Instructions
Tap on the times in the instructions below to start a kitchen timer while you cook.
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Preheat the oven to 350 degrees F (177 degrees C). Line 10 muffin cups with parchment liners.
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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.
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Recipe Notes
Serving size: 1 muffin
- This recipe was updated to make more moist muffins. 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.
- I originally made these low carb 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. The sweetener amount was also reduced from 2/3 cup sweetener to 1/2 cup, based on reader feedback.
Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.
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331 Comments
lynnita
0Do these muffins freeze well? There are just two of us here!
Wholesome Yum D
0Hi Lynnita, You can store in a freezer-safe container. Thaw at room temperature before serving.
Karen
0These are WONDERFUL!! They are so moist and flavorful. I feel like I’m cheating. Thank you for sharing this recipe.
Jessica
0The taste is there! But mine were a bit too moist. I baked for 25-26 mins, and the toothpick came out clean. But the texture is a bit squishy. After cooling, they almost fell apart in my hand trying to put them in a container. Will try again and bake longer!
Patty
0Way too much liquid a soggy Mess
Wholesome Yum D
0Hi Patty, Sorry this recipe didn’t meet your expectations. Did you follow the recipe a written? As you can see in my video, the batter shouldn’t be runny.
Jen
0Would this still work if I used pumpkin premier protein instead of the almond milk? Would like to add some protein to them!
Wholesome Yum D
0Hi Jen, I have never tried that but it should work.
Lou
0Tastes yummy – didn’t have that sweetener so used 1/2 maple syrup and added walnuts. I liked using the two flours.
Marilyn Sullivan
0I’ve tried this recipe twice. Love the flavour, but in no way does this batter turn out thick, let alone heavy. Originally I had left them to cool in their silicone cupcake holders, but they turned out soggy bottoms. So this time, I turned them out immediately only to discover they cooked with a custard like bottom. Does the recipe call for too much liquid or too many eggs? Looking for a solution 😊
Maya | Wholesome Yum
0Hi Marilyn, It sounds like they needed to bake for longer.
Christina
0Muffins were too wet and soggy, probably less eggs, milk n more flour will help and cooking temp n time.
Maya | Wholesome Yum
0Hi Christina, This sounds like they needed to bake for longer. Ovens can vary, so use the toothpick test to check when they are done.
Traci
0An alternate way I make them is 1/2 C maple syrup in place of the alluse and almond milk. The best add ins are 2 pkgs “‘Nature’s Path Superfood Oatmeal” – they’re GF and Vegan.
Always get requests for this recipe!!
Jane
0These muffins are really good and have a wonderful pumpkin flavor. I feel like they are a little too moist. I would prefer that they were a little denser. If that is the case would it be better for me to follow the old recipe? Thank you so much for your wonderful recipes!
Wholesome Yum D
0Hi Jane, If you still have that recipe feel free to use it but it is no longer on my site.
MJ Sauer
0These are fantastic. The first time I made them they were so moist they stuck to the muffin wrappers a bit. The second time I made them I put them directly into the muffin pans so that I wouldn’t lose any of the delicious muffins on the paper and they came out nicely from the pan. I also added cocoa nibs to the batter because I had them and they added a nice flavor and crunch and for me they come with less guilt than the sugar free chocolate chips 🙂 Thank you for the wonderful recipe!!
MD Houghton
0These are a Life saver for Keto Diet!
Mandy K
0I used this recipe to make breakfast bread. I was certain I had pumpkin in the cupboard but discovered I did not at the last moment. Instead, I substituted the pumpkin for unsweetened 5-seed butter and swapped the pepitas for the topping with a fine sprinkle of Serve brown sugar replacement. I baked it in a standard loaf pan at 350°F at 35mins.
Rhonda
0These sound delicious but I don’t use almond milk. Could I use no fat dairy milk instead?
Thank you!
Wholesome Yum D
0Hi Rhonda, Yes, you could use an alternate milk.
JoAnne
0This was quite tasty and I loved the nutrition profile but I didn’t love the texture. They fell apart pretty quickly, especially the next day. Is there something I’m missing? My ingredients matched your exactly (except for brands, which aren’t always the same in Canada).
Wholesome Yum D
0Hi JoAnne, The brands you use could have affected the texture of your muffins. Wholesome Yum Almond Flour and Coconut Flour are available in Canada.
Lori
0So delicious! I served them to my non-keto guests and they asked me for the recipe they liked them so much! The texture was great, light and fluffy muffins with just the right amount of ‘sweet’. I used my own blended kabocha squash in place of the pumpkin. Thank you for such a delicious treat!
Alicia
0Divine recipe! I’m on keto to lose weight, and this totally satisfied that sweet craving. I also used Earth Balance Vegan Butter (Soy free), and baked it in my convection oven for thirty minutes at three hundred twenty five degrees. Thank you, Maya, for posting this.
Carola
0These were absolutely delicious. They were very light and fluffy with great taste.
Karen
0Followed the recipe exactly (used butter) but too much butter/oil on the bottom of the muffin pan left after baking. Toothpick dry. Put them back in the oven as still too moist and cooked an additional 5 minutes. Once cooled, they were still too moist in my opinion. Next time should I reduce butter, almond milk or pumpkin purée.
Robert
0Most muffin pans are for 12 or 6 muffins. Wondering why the recipe was sized for 10 muffins. Thanks.
Wholesome Yum D
0Hi Robert, I wanted larger muffins so I only made 10, if you want to make 12 you can also do that.
Leslie Butta
0I am going to make these this week. They sound wonderful! Can I substitute heavy cream for the almond milk?
Maya | Wholesome Yum
0Hi Leslie, That should work, but I’d probably water it down a bit (and measure after watering down).
Dan H
0I tried these with heavy cream and they came out amazingly light and fluffy. Thanks for the recipe!
Kathy
0So good! Yummy and moist. I will DEFINITELY be making these again – might try some chocolate chips, or white chocolate chips next time.
Sullivan Family
0DELISH. I am always looking for delish low carb muffins. I make muffins every week! I will be adding this to my repartee of low carb muffins.
Kat
0Can I use heavy cream instead of almond milk? Can’t use anything nut based.
Wholesome Yum D
0Hi Kat, Yes, heavy cream would work.
Cecilia
0Yummy, is this recipe good for diabetics?
Wholesome Yum D
0Hi Cecilia, Yes, this recipe is low carb and suitable for a diabetic diet, but as always, consult your doctor for any medical advice.
Sandy
0Delicious. I didn’t have pumpkin seeds, so I used chocolate chips sweetened with Stevia on top.
Amy
0I love everything about these muffins! So moist and flavorful!
Anne
0Pumpkin muffins are my favorite, they are so tender and tasty.
Katie
0I love that there is a keto option for one of my favorite fall treats! Such great pumpkin and fall flavors!
Katie
0I love that these are still festive and fun for fall, but still in line with keto! So flavorful and delicious!
Natalie
0I am making these this week!! They are absolutely the best!! I have never added the pepitas on top, but what a great idea!
Rory
0I make these weekly now, they are so delicious!
Melissa in Seattle
0Simply delicious! After trying a number of keto/low carb muffin recipes, I had all but given up on finding something that I could enjoy along with my non-k/lc family. After 2.5 years, I am delighted to have the lovely aroma of baking in my home again! I also appreciate that the ingredients are all real, whole foods, unlike most of the highly processed “keto” labeled items in stores.
Note: I ended up with 13 full-sized muffins that needed 30 minutes to bake.
Thank you so much!
Janna
0Hello!
Can I make this into a loaf?
Wholesome Yum D
0Hi Janna, Yes, you can. The baking time would be a lot longer. You can also try this low carb pumpkin bread recipe.
Charlie
0These are so good Maya!!! I have been on keto/low carb for almost 4 years. Whenever I look up a recipe and see results for your page, I pretty much go straight for yours. I really love the way you combine different flours and sweeteners to get the best texture and taste possible. Allulose has become one of my favorite sweeteners too. I made my muffins a little too large I’m afraid. But very yummy. I am baking at a high altitude and find that my baked goods seem to rise a bit more than when I bake at lower altitudes. Thank you once again.
Heidi
0This is my go-to recipe in the fall! One question, I made these countless times last fall and I don’t recall the almond milk included, is that new? Thanks!
Wholesome Yum D
0Hi Heidi, This recipe has not been updated recently, maybe you are thinking of this Low Carb Pumpkin Bread that does not include almond milk.
Patricia
0Excellent recipe! Made exactly 10 muffins. Very moist and fluffy!
Baked an extra 3 minutes as my oven is new but temperamental.
This recipe is a keeper.
Thanks so much!
Janw
0I am a little confused about which fat to use – coconut oil is not solid at room temperature, so how do you measure and is it not the best option to use?
Wholesome Yum D
0Hello Janw, Pure coconut oil is solid before you melt it, so you would measure solid then melt. You can also use butter in the recipe if you prefer.
Lindsey
0I boil some water in an electric kettle and put the boiled water into a pot and then submerge my glass jar of coconut oil into the pot of water for a minute or so and it melts it enough to pour out how much I need into a liquid measuring cup!
Kerry
0Thanks for this recipe! The mix of equal flour portions gave these muffins a more traditional bread-like texture. We added just a bit of molasses, which raised the carb count by roughly 1.3 grams (our batch made 12 muffins). We cut the sweetener to 1/3 cup instead of 1/2 (my wife likes less sweet baked goods), and this gave a slightly sweet, but still delicious, muffin. We enjoyed them with a cup of pumpkin spice coffee. A great start to a cool fall morning!
Jann
0Can I just use almond flour?
Wholesome Yum D
0Hi Jann, I haven’t tested this particular recipe without coconut flour and it’s crucial for the right consistency here, but I do have lots of keto almond flour recipes here, many of which don’t call for any coconut flour.
Susan
0The muffins turned out great and I enjoyed making them. They tasted wonderful fluffy and moist. Will definitely make it throughout fall and winter.
Nanette
0Mine came out to be a little bland and not the consistency of a typical muffin. Had to eat it with a fork. Put a bit of butter on top while still hot, that improved the taste. Disappointing. Followed the directions to a T.
Maya | Wholesome Yum
0Hi Nanette, You mentioned putting butter on while still hot, so I assume you tried the muffins while still hot. Let these cool first for best results in terms of texture. You can still reheat afterward if you prefer a warm muffin. Hope this helps!
Petra
0I’ve got these in the oven right now and can’t wait. They are rising nicely and look delicious. I’m sure they will be a delightful dessert for after dinner tonight. Thanks, Maya!
Deb
0These are delicious! I used unsalted butter and also turned the oven temperature down a bit. Will definitely make again.
Cat
0Second time making them and they were perfect each time !
Beth
0Can I use ALL almond flour rather than mixture?
Wholesome Yum D
0Hi Beth, I haven’t tested this particular recipe without coconut flour and it’s crucial for the right consistency here, but I do have lots of keto almond flour recipes here, many of which don’t call for any coconut flour.
Raven Dedola
0Can you make this recipe with all coconut flour? I have family members who are allergic to nuts, (almond flour).
Wholesome Yum M
0Hi Raven, Sorry that won’t work in this recipe. If you would like to use just coconut flour, check out this recipe for Pumpkin Pie Cupcakes.
Christina
0Excellent! No changes to recipe and came out perfect! (I used coconut oil instead of ghee) Moist and tasty. And very pretty too!
Catherine
0I never cared for pumpkin spice. I was looking at an old issue of women’s world and they had an article on Thyroid detox and a recipe for pumpkin spice thyroid booster muffins. Yum they were good. After I ate them all I looked up keto pumpkin spice muffins. You recipe came up. Just made those today. Loved those too! Thanks. And LOVE your keto ranch dressing.
Claire Anderson
0Hi, I was hoping you could clarify your point regarding the coconut oil option, recommending it not be at room temperature.
I’m a bit confused by this as In the receipe it calls for it to be measured solid then melted, so does that mean I put in in with the other ingredients hot? Really?
Thank you
Wholesome Yum M
0Hi Clarie, Not hot, but melted. Coconut oil is used as a liquid in this recipe and melts just above room temperature.
Deb
0Coconut oil is liquid in a hot as in summer hot temperature but turns solid with cooler temps. We live in ny, our coconut oil is solid most of the year but liquid during the warm months.
Doreen
0This were so delicious. A bit falling apart, but oh so yummy. I mixed up some cream cheese with stevia drops and vanilla. So good!