Free Printable: Low Carb & Keto Food List
Get It Now- Why You’ll Love This Low Carb Keto Pumpkin Muffins Recipe
- Almond Flour Pumpkin Muffins Ingredients
- How To Make Low Carb Almond Flour Pumpkin Muffins
- Tips For The Best Low Carb Pumpkin Muffins
- Variations
- Storage Instructions
- More Low Carb Pumpkin Recipes
- Tools To Make Pumpkin Keto Muffins
- Low Carb Keto Pumpkin Muffins Recipe Recipe card
- Recipe Reviews
Low 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.
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.
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.
Did You Like It?
Leave a rating to help other readers (this also helps me continue to provide free recipes on my site), or get the recipe sent to your inbox.
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.
© 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. 🙂
334 Comments
Erika
0These satisfied my all-things-pumpkin-spice FOMO! The flavor, texture, and moistness is perfect. I melted Kerrygold salted butter for the oil. The muffins baked up beautifully in 25 min. and no issues with over-browning.
Pam Kirsch
0These pumpkin muffins are absolutely delicious!! They are so moist and flavorful! I had 2 right out of the oven with butter – yum. Tomorrow I’m going to make some pecan or walnut cream cheese spread to put on them – can’t wait. Thanks for another fabulous recipe!
Nicola
0Made this recipe tonight and it turned out AMAZING!! I also added some cream cheese mixed with erythritol into the centre of each muffin and o m g it was soooo good. Thanks for the fab recipe – will defo be making again 🙂
Sandra
0I have tried many of your recipes but today i made these and mixed up a basic cream cheese icing and I thought I went to heaven. Absolutely loved it!!! Second only to your famous cheesecake recipe. Thank you!!
Linda Sanders
0Love these muffins. I made them this week for a team lunch and they were a hit!
Laura
0These pumpkin cupcakes are awesome!!! So moist, tender, packed with flavor. I put sliced almonds on top. They’re a big hit everywhere I take them!! Nobody can believe they’re low carb!!! Thanks so much for this recipe. I’ve made other recipes on your site and they’re all sooooo good!! Thanks so much.
Kim
0These sound fantastic!! I need egg free. Have you ever done flax eggs or chia eggs?
Wholesome Yum M
0Hi Kim, Other readers have had success making these with flax eggs. It was noted that they may need to bake longer than the listed time in the recipe. Enjoy!
Kayla Mcintyre
0Hi I’ve been trying to find a recipe with just almond flour and couldn’t!! I don’t use coconut flour, and was wondering if I can just use almond flour? Thank you. I’ve been dying to try this recipe
Wholesome Yum A
0Hi Kayla, the coconut flour is necessary in this recipe to absorb moisture from the pumpkin. You might have better luck modifying this recipe to include pumpkin pie spice and pumpkin seeds instead of blueberries.
Karen Shaw
0If I were to add a non-keto sweetener, e.g. maple syrup, brown sugar, or honey, do you know how much I should use in this recipe? Thanks!
Wholesome Yum A
0Hi Karen, I don’t work with those sweeteners much so I’m not sure. Be aware that substituting granulated sweeteners with liquid ones may also change the final texture.
Natalie
0Had these muffins at a friend’s & asked for the recipe because they’re soo good! I added 60% cacao chips too. I used monkfruit sweetener. They came out really well & I cant wait to try your other recipes. I’ve been reducing my carb intake recently-paying attention to the numbers. This treat really helps me to not “lose it” -meaning to keep me from falling off the low carb wagon! Thanks for your research & sharing your recipes! Thank you?
Tonia
0I’ve been exploring options for my 4 year old, who was recently diagnosed with Type 1 diabetes & is the pickiest eater alive! I have tried sooo many recipes but this is the only thing he’s actually liked (& eaten)! I can’t tell you what it means to have even one healthy option for him as his blood sugar levels are a constant battle. I look forward to trying more of your recipes!
Sierra
0Hi! I’m a huge fan of your pumpkin bread recipe and thought I would use this one for muffins! However, it calls for 1 tbsp of baking powder, which is almost double what your bread recipe uses.. could this be a typo? I made the recipe last night and am noticing that the taste seems off.
Wholesome Yum M
0Hi Sierra, Thanks for checking! The amount of baking powder listed is correct.
Peg
0All I can say is, “WOW!” These were absolutely amazing! They were fluffy, flavorful and such a great treat for a lazy Saturday. I substituted xylitol for the sweetener, which did add a few carbs but I’m a little burned out on the taste of Swerve. I also topped the muffins with walnuts instead of pumpkin seeds and used butter instead of ghee. The batter was very thick and required 32 minutes total baking time, but the end product was truly amazing. Thanks for letting me have a little treat without blowing my low carb eating plan!
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?
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.
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.
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!
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!