Gluten-free pumpkin muffins that rival their glutenous counterparts! These GF muffins boast a floofy, tender crumb, not-too-sweet taste, and just the right amount of pumpkin spice. Free of refined sugar, gums, and nuts, with tested dairy-free, vegan, and low-fodmap options too.
Thanks to Bob's Red Mill for sponsoring this post! All opinions are my own.
These gluten-free pumpkin muffins officially hold the title of most tested recipe on TBG. Guess how many times I tested them ?
Fourteen. Fourteen times. I thought I was going to turn into a pumpkin muffin. Thankfully they're so delicious that even the textural fails got devoured, warm from the oven, without too many complaints.
In Search of the Best Gluten-Free Pumpkin Muffin Recipe
A GF muffin recipe wouldn't normally take me so many tries, but I wanted the recipe to be accessible to as many folks as possible. I adapted the recipe from my favorite gluten-free pumpkin bread which uses a good number of eggs to help fluff up and set the crumb. But I know that many of my readers also have egg allergies. So I set out to find a formula that would work equally well with flax egg, my preferred egg substitute since I always have flaxseed meal on hand. I also wanted these muffins to be naturally sweetened with unrefined sweeteners, and free of gums.
With a little help from Yes, Please Bakes, who's a pro at allergy-friendly baking, I experimented with different ingredients and ratios. I tried a grain-free paleo version using almond and cassava flours, but I ended up settling on my go-to blend of grain flours: millet, oat, and sweet rice, plus some tapioca flour. I tried different flax egg ratios and methods. I tinkered with maple syrup and coconut sugar as sweeteners, and eventually landed on using some of each.
I'm so excited to share the results. These GF pumpkin muffins are everything I'm craving right now. They're:
- full of warming spices
- naturally and minimally sweetened
- easy and quick to make
- über-flavorful
- moist, springy, floofy, and tender
- vibrant and golden with pretty crackled tops
- free of gluten, gums, nuts, refined sugar (and optionally dairy and eggs)
Most of the photos shown here are of the eggy, dairy-y muffins, but keep scrolling for a side-by-side comparison of the vegan gluten-free pumpkin muffins!
Ingredients and Substitution Suggestions
- A whole cup of pumpkin puree adds moisture and nutritional value. Be sure you're *not* using pumpkin pie filling which has other ingredients in it. You can use homemade winter squash puree if you prefer (butternut tends to be closest in texture to canned pumpkin).
- Eggs help these gluten-free pumpkin muffins bake up extra fluffy. For vegan pumpkin muffins, replace the eggs with flax eggs (2 tablespoons flaxseed meal mixed with 1/4 cup + 2 tablespoons hot water; let sit until thick, 10-20 minutes.)
- Coconut sugar and maple syrup sweeten the muffins, making these free of refined sugar. You can swap any granulated sugar for the coconut sugar (date sugar, maple sugar, or granulated white or brown sugar) and any liquid sweetener for the maple syrup (such as coconut nectar, agave, or date syrup).
- Olive oil makes these moist and tender. I use a mild-tasting olive oil, though any liquid oil will work including sunflower, grapeseed, or avocado oils.
- Sour cream or Greek yogurt add moisture and tenderness. Use plant-based versions, or a rich coconut yogurt, in their place for dairy-free.
- Golden pumpkin spice mix adds bright, spicy notes, with turmeric enhancing the golden glow of the crumb. One batch of the mix makes enough for 4 batches of these muffins, but I've included spice measurements for a single batch in the notes if you prefer. Get the pumpkin pie spice recipe here!
- Baking soda and baking powder add lift and help the tops brown.
- Fine sea or kosher salt makes the flavors pop.
The best flours for gluten-free muffins:
A few gluten-free flours work together to create an airy, springy crumb with some hearty whole-grain flavor. I use Bob's Red Mill flours which are milled in a certified gluten-free facility.
- Gluten-free oat flour adds whole-grain flavor, fiber, and protein, while making the crumb tender and fluffy.
- Sub by weight sorghum flour or teff flour.
- Sweet rice flour is more starchy and sticky than regular rice flour and it helps the muffins hold together with a springy crumb.
- Sub by weight gluten-free all-purpose flour (such as Bob's Red Mill 1 to 1) or cassava flour.
- Millet flour has a golden hue, fine grind, and buttery taste that compliments the pumpkin beautifully.
- Sub by weight sorghum, teff, or buckwheat flour.
- Tapioca flour makes the crumb extra plush and pillowy.
- Sub by weight arrowroot flour.
How to Make Pumpkin Muffins
Once you've gathered your ingredients, gluten-free pumpkin spice muffins will be yours in under an hour! These are so easy to make.
Gluten-Free Pumpkin Muffins for Everyone: Allergy-friendly options
These healthy gluten-free pumpkin muffins are refined sugar-free, nut-free, and gum-free. I've tested the following versions to make them even more allergy-friendly.
Dairy-Free Pumpkin Muffins
Use plant-based sour cream, Greek yogurt, or rich coconut yogurt in place of the sour cream. I tested these with Cocojune plain yogurt, which is made with just coconut, cassava root, and cultures. My other favorite brand is Culina.
Egg-Free Pumpkin Muffins
Make flax eggs by combining 2 tablespoons flaxseed meal with 6 tablespoons hot water and let sit until thick.
Vegan Pumpkin Muffins
Use plant-based dairy and flax eggs.
Here's a side-by-side comparison of the regular recipe (left) next to the vegan recipe (right). The vegan muffins are a little more delicate and slightly more dense, but still completely delicious.
Low-FODMAP Pumpkin Muffins
These muffins also happen to be low-fodmap, for those following a low-fodmap diet for medical reasons. For fewer fermentable carbs, use lactose-free sour cream and swap the coconut sugar for maple sugar or organic granulated sugar.
Paleo Pumpkin Muffins
I have yet to perfect a grain-free version of these pumpkin muffins, but I highly recommend these paleo pumpkin muffins from my friend Aysegul at Foolproof Living. Or try these flourless pumpkin muffins from my friend and nutrition coach Alison at Food by Mars.
Variations
A few ideas to play with!
Gluten-Free Pumpkin Chocolate Chip Muffins
Stir 1/2 cup dark chocolate chips or chopped bittersweet chocolate into the batter.
Gluten-Free Cheesecake Muffins
Back in my first year of blogging, before I had a good camera or any photography experience, I shared a glutenous pumpkin cheesecake muffin recipe. Use that cheesecake filling and method with this batter and you'll have yourself some gluten-free pumpkin cheesecake muffins! I'd recommend making the batter into 14 muffins since the cheesecake filling will add extra volume.
Gluten-Free Pumpkin Cupcakes
Omit the cinnamon sugar sprinkle and top the baked muffins with low-sugar cream cheese frosting, vegan cream cheese frosting, or paleo cream cheese frosting for healthier gluten-free pumpkin cupcakes.
GF Pumpkin Streusel Muffins or Pumpkin Crumb Muffins
Make a batch of gluten-free streusel and use it to top the muffins instead of cinnamon sugar.
Gluten-Free Pumpkin Coffee Cake
Spread the batter in a 9-inch springform pan and top with gluten-free streusel for pumpkin coffee cake dreams. You could fold some fresh cranberries into the batter if you liked!
Serving Suggestions: How to Eat Pumpkin Muffins
These tender oat flour pumpkin muffins need little accompaniment, but here are some ideas for how to enjoy them even more:
- slather with salty butter or plant butter
- drizzle with maple syrup or honey
- sprinkle with more cinnamon sugar
- schmear with softened cream cheese (dairy or plant-based)
- drizzle with maple glaze
- warm, cut in half, and top with a scoop of vanilla ice cream (or maple ice cream, buttermilk ice cream, ginger ice cream, or horchata ice cream) for dessert
- accompany with mugs of apple cider hot toddies or vegan gingerbread lattes
Make-Ahead Muffins
These gf pumpkin muffins freeze beautifully. Here's how:
- Place the cooled muffins on a small baking sheet and place in the freezer until they're firm.
- Transfer to a freezer-safe container or zip-top bag and store for up to 2 months.
- To enjoy, place a frozen muffin in a 325ºF oven or toaster oven until heated through, 10-15 minutes.
However you serve up these gluten-free pumpkin muffins, I hope you enjoy them as much as we do!
More Gluten-Free Pumpkin Desserts
- Gluten-Free Pumpkin Bread (DF)
- Gluten-Free Pumpkin Cream Pie (DF & vegan options)
- GF Pumpkin Pouding Chomeur (baked pudding cake)
- Pumpkin Buttermilk Pie
- Gluten-Free Pumpkin Cheesecake Brownies
- Pumpkin Pudding (DF & vegan options)
- No-Bake Pumpkin Pie (GF, vegan & paleo)
- Gluten-Free Pumpkin Nut and Seed Bread (from Alternative Baker via Foolproof Living)
- Find all of my favorite gluten-free pumpkin desserts here!
More Gluten-Free Muffins and Quickbreads:
- Gluten-Free Chocolate Chip Banana Muffins
- Vegan & Gluten-Free Nut and Seed Bread
- Paleo Vegan Chocolate Banana Bread
- Vegan Grain-Free Banana Bread
- Paleo Zucchini Bread (vegan)
*Bojon appétit! For more Bojon Gourmet in your life, follow along on Instagram, Facebook, or Pinterest, purchase my gluten-free cookbook Alternative Baker, or subscribe to receive new posts via email. And if you make this vegan gluten-free pumpkin muffin recipe, I’d love to know. Leave a comment and rating below, and tag your Instagram snaps @The_Bojon_Gourmet and #bojongourmet.*
Gluten-Free Pumpkin Muffins (dairy-free & vegan options)
Print Recipe Pin RecipeIngredients
Muffins:
- 2 large eggs (see note for vegan option)
- 1 cup + 2 tablespoons (258 g) pumpkin puree
- ½ cup (100 g) mild olive oil (or other neutral oil such as sunflower or grapeseed)
- ¼ cup (36 g) coconut sugar (or maple sugar, date sugar, or granulated or brown sugar)
- ¼ cup (76 g) maple syrup
- ¼ cup + 2 tablespoons (90 g) sour cream or full-fat Greek yogurt (use plant-based for dairy-free)
- ¾ cup (75 g) Bob's Red Mill gluten-free oat flour*
- ½ cup (80 g) Bob's Red Mill sweet rice flour**
- ½ cup (60 g) Bob's Red Mill millet flour***
- 2 tablespoons + 2 teaspoons (20 g) Bob's Red Mill tapioca flour
- 2 ¼ teaspoons baking powder
- ½ teaspoon baking soda
- ¾ teaspoon fine sea or kosher salt
- 1 tablespoon golden pumpkin spice mix****
Topping:
- 1 tablespoon maple or coconut sugar
- ½ teaspoon ground cinnamon
Instructions
- Position a rack in the upper third of the oven and preheat to 350ºF. Line 12 standard-sized muffin cups with paper liners or rub with room temperature butter or coconut oil.
- In a large bowl, whisk together the egg, pumpkin puree, olive oil, coconut sugar, maple syrup, and sour cream until smooth.
- Place a strainer over the bowl and sift in the oat, sweet rice, millet, and tapioca flours with the baking powder, baking soda, salt, and spices.
- Whisk the batter until smooth. Let sit for a few minutes to thicken (this makes it easier to scoop into the cups) and use a large spoon or spring-loaded ice cream scoop to fill the muffin cups almost to the top. Gently smooth the tops.
- Mix together the maple sugar and cinnamon and sprinkle over the tops of the muffins.
- Bake the muffins until the tops are domed, spring back when poked, and a toothpick inserted in the middle of a muffin comes out with moist crumbs, 20 – 30 minutes.
- Let the muffins sit for a few minutes to firm up, then carefully remove them to a wire rack to let them cool.
- They are most delicious within a few hours of baking, but will keep, covered, at room temperature for a day or too. Refrigerate or freeze for longer storage.
Notes
- 1 1/8 teaspoons ginger
- 1 teaspoon cinnamon
- 1/4 + 1/8 teaspoon nutmeg
- 1/4 + 1/8 teaspoon turmeric
- 1/8 teaspoon allspice
Nutrition
Golden Pumpkin Spice Blend
Print Recipe Pin RecipeIngredients
- 2 tablespoons ground ginger
- 1 ½ tablespoons ground cinnamon
- 2 teaspoons ground turmeric
- 2 teaspoons nutmeg (freshly grated if possible)
- ½ teaspoon ground allspice
Instructions
- Combine ginger, cinnamon, turmeric, nutmeg, and allspice in a bowl or jar.
- Stir or shake to combine.
- Store airtight at room temperature for up to 1 year.
Notes
- 1 teaspoon ground cardamom
- 1/2 teaspoon ground cloves
- 1/4 teaspoon ground black pepper
Emma says
Legitimately the best pumpkin muffin I have ever made. Not too sweet, texturally super fluffy and perfect, just YUM! Also it's so hard to believe they're free of refined sugar, gluten, and dairy -- you'd never know it. These will be on repeat ALL fall (and winter...and spring...and probably summer because who am I kidding).
Alanna says
Aww thank you *so much* for testing this recipe Emma! I'm so glad you guys loved them!! You're not the only one who's pumpkin-happy all year round. :)
Trish says
Alanna, you read my mind! I have been looking for some “fallish” recipes to make for the farm for which I bake. And as I read your post I was wondering if I could put cream cheese in some form in the center and you answered that! This is on my must do list within the next two days. Can’t wait! Thank you!
Alanna says
Aha, fabulous!! Pumpkin cream cheese muffins were a childhood favorite of Jay's too. Please keep me posted on how they turn out!
Alene says
Good morning! You remember I have this rice thing going on. A British blogger's book gave me a rice free blend that actually worked perfectly in her pumpkin bread. I was ecstatic. It's a lot of tapioca flour, and less of buckwheat and millet. It actually tastes like it was made with a.p. flour. I had tried cassava on something of yours for the sweet rice flour but it fell apart. It might have been your honey cake. I think I'm going to make these but change the rice to all tapioca, including the 2 T + 2 tsp you have in the recipe. I was very surprised hers came out so good. I adore pumpkin too, so as soon as I finish the bread, I will bake your muffins with that change and let you know. And I'm glad it's raining there. It must be a relief.
Alanna says
Hi Alene! That sounds like a great blend and recipe! Which book is it from? I'd love to check it out.
Please let me know how the muffins turn out using tapioca flour in place of sweet rice. I'm curious to try it that way too now!
Yes the rain was very light but still felt completely delicious. Hopefully it will help keep wildfires at bay for a bit.
Sarah says
Omg, these look amazing and I LOVE your commitment to experimenting with as many variations as possible so people with various restrictions and sensitivities can still enjoy 💜💜💜💜💜. THE specific suggestions like replacing sweet rice with cassava will be handy, depending on what I have stashed in the pantry on any given day… although let’s be honest I have about 15 different flours right now. 😭
I esp appreciated the photo showing the difference between the vegan and egg-full options, I eat eggs and dairy just fine, but when I need something that is both gluten free and vegan it can feel like chasing the holy grail.
Alanna says
Aw thank you so much Sarah! Please let me know what you try and which of your 15 flours you use haha. I feel you!
Sid says
Hello! This is a bit off-topic, but while we talking cozy holiday flavors, I was wondering: do you have any good sugar cookie recipes up your sleeve? I love your ginger cats recipe, but I also want to make some basic light-colored cookies to complement them. The GF sugar cookie recipes I’ve tried from elsewhere (not naming any names here) have generally turned out to be sad, crumbly messes.
Alanna says
Hi Sid! I'm so glad you love the ginger cats. I haven't made an GF sugar cookies yet, but now I want to! You're thinking of a rolled, cut-out type of cookie that you could frost for the holidays right? Sarah at Snixy Kitchen has a GF sugar cookie recipe that might be a good bet. But I'll let you know if I experiment! Appreciate the request - let me know if you have any more! :)
Sid says
Yes, that’s exactly the type of cookie I’m looking for! Something easy to stamp out and decorate. Would love to see what you could dream up. In the meanwhile, will check out Sarah’s recipe.
Speaking of holidays, I’m also thinking about putting my gingerbread architectural skills to the test — I bet the ginger cats recipe would have the structural integrity to make some miniature load-bearing walls, don’t you think?
Also — I tried the muffins and must have messed something up along the way, as they rose but sank back down into an almost pudding-like texture, like the inside of a soufflé. They were still delicious and we ate them all, though. I halved the recipe and am wondering if I did something wrong with the math, or if I let the batter sit out for too long before popping it in the oven (I got distracted and it sat out for 30 mins before baking). Will try again with a little more care.
(Also also — I made the corn spoon bread last week and oh my god, it’s going to become a part of my regular rotation. I could have gone face-first into the thing but I had to share it.)
Alanna says
Aw I'm so glad you loved the spoon bread – I'm totally craving that now!
Hm I'm not sure about the ginger cats as gingerbread house, but it would be worth a try? It would be a delicious mess at the very worst!
I'm sorry the halved muffin recipe gave you trouble! I actually tested this recipe a zillion times as a half batch, so it should definitely work. I have the quantities typed up and can email them to you if you like, just let me know.
Tanya says
I just made these for the second time in a week. In the oven now, but I forgot the cinnamon sugar topping before I put them in this time! Everyone in my house loves these & they are perfect as we have one member with celiac. Both times I’ve made these I wanted to use the whole can of pumpkin so I added just enough apple sauce to double the pumpkin weight & squeezed a double recipe out of 1 can of pumpkin. They taste amazing, although I am sure they are better if I follow your recipe exactly. If I ever use baked pumpkin & have enough, I’ll leave out the apple sauce.
Alanna says
I'm so glad you love this recipe Tanya! Doubling the recipe to use a full can of pumpkin and adding in a little applesauce to make up the difference is totally brilliant. You might be able to brush the tops with a little melted butter and sprinkle them with cinnamon sugar after the fact if you like! Thanks very much for trying my recipe and for the sweet note!
Stephanie says
These are delicious. I used teff instead of millet. Next time I make them I will use more sugar.
Alanna says
I'm so glad you liked them! You can absolutely use more sugar to your taste. I'd recommend trading out some of the sour cream so that the batter doesn't become overly wet. So if you add 2 tablespoons sugar, try reducing the sour cream by 2 tablespoons. Let me know what you try!
Elizabeth says
Did I miss something? Reading the recipe, it says for 12 muffins, but it also says "Line 6 standard-sized muffin cups".
Alanna says
Aha, good catch! I fixed that typo - it's 12 muffins. :)
Trish says
Alanna, another winner! Light and moist and flavorful and I’m afraid I’m going to eat too many if someone doesn’t stop me! Your recipes have made gf baking a delight and so much better than I could have dreamed, even five years ago. Can’t wait to try your suggested variations. Good work!
Alanna says
You are the sweetest Trish! Thanks for giving the muffins a go - I'm so glad you loved them. Too many pumpkin muffins, said no one ever! ;)
Trish says
This afternoon I tried the muffins with the streusel topping and they are delicious! I used about half of the streusel recipe and liked it but how could using more be bad? ;-) Next, I’m trying them with your cheesecake filling. Can’t wait!
Alanna says
I wish we were neighbors and that I could come pilfer a couple of streusel muffins - that sounds so good! Please let me know how the cheesecake filling goes - YUM.
Catherine says
Hi Alanna,
I usually love your recipes but this one didn't work for me for some reason. I made the vegan version (with sorghum instead of millet) and they ended up really gummy - like mochi muffins. They were definitely not under baked so it's not that. Any thoughts? The flavor was great so I want to figure these out!
Thanks again for the great recipes you provide.
Alanna says
Well that's no good - I'm so sorry that happened! Yes, happy to help troubleshoot.
What did you use for the sour cream/yogurt (type and brand)? Did you measure the ingredients by weight or by volume?
Those are the two main variables that I can think of. It's possible that the sorghum flour isn't as absorbent as the millet flour and could have contributed to the funky texture.
Hopefully we can figure it out and get you some non-gummy muffins!
Catherine says
Thanks for getting back to me! Yes I measured everything by weight. I used the Kite Hill Blissful coconut yogurt - is there a specific vegan yogurt you recommend? I did use canned pumpkin, as well but usually that doesn't matter much.
Alanna says
Hm you did everything just right! I've never had that coconut yogurt but it sounds like it *should* work fine, although it contains some gums and starches which may have contributed to the mochi-like texture. I wonder if Kite Hill greek yogurt would work any better.
I'm planning to get some greek yogurt and coconut yogurt to test in this recipe side by side this weekend, so stay tuned. I have some canned pumpkin in the fridge that I need to use up anyway!
Catherine says
Thanks so much. I can't wait to see what you find!
Alanna says
Ok, I tested two half-batches today; one with Kite Hill Greek almond yogurt, and one with Cocojune coconut yogurt (made with just coconut, cassava root, and cultures). I haven't been able to find Kite Hill coconut yogurt at my local stores unfortunately. I stuck with the original flours and used millet.
Both yogurts worked well, though the muffins made with coconut yogurt were more rich and tender and had a sweeter taste. I liked these best!
The ones with almond Greek yogurt were sturdier and a little less sweet.
Both versions do have a slightly more mochi-like texture than when made with dairy and eggs. It's so hard to mimic eggs' structure and stickiness, and so the flax does add a bit of chew. But they're definitely lighter and less dense/chewy than actual mochi cake.
It's possible that the sorghum flour and Kite Hill's coconut yogurt, which has more gums in it, made the muffins extra chewy? It might be worth trying them with millet flour and/or coconut yogurt with fewer gums (Coyo, Culina, and Cocojune are my favorite brands) to see if that helps them texturally. Maybe test a half batch in case it doesn't help! I can email you the half batch recipe with weights if you like for ease!
Alternatively you could try upping the oat and sorghum/millet flour and decreasing the sweet rice flour to see if that makes them less chewy.
I hope this is helpful! Let me know how else I can help!
Catherine says
Thank you for testing! I will try millet + other yogurts and report back.
SJ says
I made this into a coffee cake-- with a layer of halved cranberries and topped with a streusel (a mix of your blueberry coffee cake and pumpkin granola recipe). I baked it in a 6 inch cheesecake pan (one with a removable bottom) and it took a little over an hour. It came out great! Next time, I think I'll toss the halved cranberries with a few tablespoons of the dry mixture next time to sop up all the juices they release while baking. Thank you!
Alanna says
Hi SJ! That sounds completely divine. Save me a slice! Tossing the berries with a little extra flour sounds like a good call. You could also take down the dairy by a couple of tablespoons if that sounds helpful! Let me know if you make it again. :)
SJ says
Thank you! I made a half batch for my next attempt (I ate the equivalent of 12 muffins in days!!!) to curb overeating. I realized that recipe called for Greek yogurt instead of regular yogurt which might have led to the first batch being a bit soggy in the center. I baked the half recipe in the loaf pan and omitted the maple syrup since I used a honeynut squash which is sweeter, and didn't reduce the Greek yogurt amount (well, just my half for the half recipe). It came out much less soggy :). I think my next iteration will be a gingerbread version-- using maple and molasses (and reducing the Greek yogurt) and using gingerbread spices instead of the golden pumpkin spice (which I love). And I'll try making them in muffin tins to see if that impacts the bake-- the recipe is so delicious I don't mind testing! I give all food blogger kudos for all the testing/troubleshooting in developing recipes-- there are so many variables that go into a recipe! Thank you again!
Alanna says
Awww thanks for the kind words! Yes there are *so* many variables in baking. I'm so glad the Greek yogurt turned out better!
I absolutely LOVE the idea of the pumpkin gingerbread – now craving that big time! Please let me know how it turns out.