Healthy Gluten-Free Pumpkin Muffins

GFGluten FreeNFNut FreeOFOil FreeSFRefined Sugar FreeVVegan
4.88 from 32 votes
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Fluffy and moist, these Gluten-Free Pumpkin Muffins are the perfect pumpkin-filled treat! They’re healthy enough breakfast, delicious enough for dessert, and packed with cozy fall flavors. Vegan, Gluten-free, Oil-Free, Refined-sugar free and Nut-free options.

These Gluten-Free Pumpkin Muffins are hands down the best, fuss-free gluten-free muffins! They’re made with budget-friendly and wholesome ingredients, yet perfectly moist and fluffy with a tender crumb. These healthy pumpkin muffins are simply a must make during pumpkin season (or any time of the year!).

Table of Contents
  1. Moist, Fluffy Fall Muffins Made in 1-Bowl!
  2. What You Need for Gluten-Free Pumpkin Muffins
  3. How to Make Gluten-Free Pumpkin Muffins
  4. Serving Suggestions
  5. How to Store Gluten-Free Pumpkin Muffins
  6. Substitutions and Variations
  7. Recipe FAQs
  8. Healthy Pumpkin Muffins (Gluten-Free) Recipe
three muffins stacked on top of each other on a small white plate

Moist, Fluffy Fall Muffins Made in 1-Bowl!

If you’re the #basic Fall lover (like me) and stock up on pumpkin puree as soon as the temperatures start to drop, you’re going to LOVE these pumpkin muffins. They’re inspired by my moist and fluffy Vegan Pumpkin Bread, but are made 100% gluten-free, oil-free, and can be made refined sugar-free, if desired. Despite the lack of gluten, I think you’ll agree they’re just as moist and fluffy as classic muffins. Plus, they’re stuffed with good-for-you ingredients, warm, fragrant spices, and real pumpkin flavor. Not to mention, they’re made in just 1 bowl (dish-washing haters, rejoice!). What could be better?

What You Need for Gluten-Free Pumpkin Muffins

I tried to keep things as budget-friendly and as accessible as possible, without sacrificing taste or texture. In addition to the basic pantry ingredients like sugar, non-dairy milk, and leavening agents, these muffins get their magical moisture and rise from 3 key ingredients: 

ingredients for the pumpkin muffins laid out on a marble kitchen countertop
  • Pumpkin puree: Pumpkin puree gives these muffins a delightful fluffiness and moisture without adding too much sweetness. Just make sure to buy the plain canned puree, not Pumpkin Pie mix.
  • Nut or seed butter: Keeps these muffins oil-free, while still adding some creaminess. The key is to use runny butters. Otherwise, your muffins will be on the dry side.  
  • Oat flour: Ground oats is my go-to in gluten-free baking because it’s cheap, easy to make, and gives baked goods the perfect balance of fluffiness and chew. You can purchase pre-made oat flour in most grocery stores, but I prefer to make it at home – just blend the oats in a high-speed blender for 45-60 seconds, or until a fine flour forms. 
  • Finally, you’ll (of course) need a heaping tablespoon of pumpkin pie spice for all the pumpkin spice flavor. You can even sprinkle some ground cinnamon in there for an even greater flavor punch! 

How to Make Gluten-Free Pumpkin Muffins

side-by-side images of the baking process of pumpkin muffins
  1. Blend the oats into a fine flour.
  2. In a large bowl, mix the wet ingredients together until thick and combined. 
  3. Add the dry ingredients and mix ​well. 
  4. Fold ​in the walnuts or chocolate chips. 
  5. Fill the muffin liners, then sprinkle the top of the muffins with additional nuts, pumpkin seeds, or dairy-free chocolate chips.
  6. Bake ​for 30 to 32 minutes, until fluffy and golden. 
  7. Let cool completely on a wire rack, then enjoy!

Caitlin’s Cooking Tips

  • Gluten-free muffins require a longer bake time. If you’re accustomed to baking muffins with all-purpose flour, you may be surprised by the bake time. Gluten-free muffins take significantly longer to bake (almost twice the amount of time!) because their delicate crumb structure (aka fluff) takes significantly longer to develop. 
  • Measure the oats before grinding. ​This matters less if you are using the weighted measurement, but for the most accurate measurement, it is best to measure the rolled oats before grinding them. 
  • Use a cookie scoop to divide the muffin batter. Filling muffin liners with pumpkin muffin batter is infinitely ​easier with a cookie scoop. Yes, a spoon works, but once you use a cookie scoop, you’ll never go back! It’s quick, easy, clean, and just all-around the best way!
pumpkin muffins laid out on a cooling rack

Serving Suggestions

These gluten-free and vegan pumpkin muffins are healthy enough to enjoy for breakfast alongside morning coffee, as well as a wholesome afternoon snack. However, they can also be served as dessert alongside a hearty scoop of your favorite non-dairy ice cream and a drizzle of creamy nut butter, Pumpkin Spice Maple Syrup, or Salted Caramel Sauce

If you’re looking for more gluten-free pumpkin recipes, you’ll also love this Pumpkin Chai Bubble Tea, these Pumpkin & Chai Spiced Donuts, and these Gluten-Free Pumpkin Spice Waffles!

How to Store Gluten-Free Pumpkin Muffins

These gluten-free muffins will keep best when stored in an airtight container at room temperature for up to 5 days. For longer storage, freeze muffins for up to one month in an airtight freezer bag. If you like to enjoy your muffins warm, they can be microwaved for 5-10 seconds, or placed in a toaster oven and heated until just warm. Be careful not to over do it or your muffins will become dense and dry.

Substitutions and Variations

  • Brown sugar substitution: Use an equal amount of coconut sugar, or another granulated sugar. 
  • Nut-free option: I like to use either runny Almond Butter or Peanut Butter for these muffins, but you could also use Tahini or melted Coconut Butter if you have an allergy.
  • Homemade pumpkin puree: Is your grocery store out of pumpkin puree? Replace the canned pumpkin with 425 grams of Homemade Pumpkin Puree. If the homemade version appears more wet and runny compared to canned pumpkin, blot it with paper towels before until the pumpkin puree is thick enough to stay rounded in a mound when you scoop it with a spoon.
three muffins stacked on top of each other on a small white plate

Recipe FAQs

Can I make these muffins with a gluten-free flour blend?

Unfortunately, no. Gluten-free baking is incredibly precise and each gluten-free flour has a unique absorption rate. Replacing the oat flour with another gluten-free flour such as almond flour or flour blend will change the end results drastically and likely not in a good way. If you only have a gluten-free flour blend, make these Pumpkin Cornbread Muffins instead.

Does canned pumpkin have gluten?

It shouldn’t. Pure pumpkin puree should contain just one ingredient – pumpkin. For my canned pumpkin recommendations, make sure to check out my Canned Pumpkin Comparison. If you have celiac disease and are concerned about contamination, always check with the specific brand for details on processing.

How many muffins does this recipe make?

As written, this recipe makes 12 regular-sized muffins. The muffin cups will be rather full, but all batter should fit in a standard-sized muffin pan. A reader has also shared baking these muffins into 18 mini muffins, but we have not tested this ourselves.

Can I reduce the sugar in these muffins?

You should be able to use less sugar without issue, so long as the amount you reduce is not a lot. Otherwise, you may need to compensate with more oat flour to prevent the muffin batter from being too moist.

I am not gluten-free. Can I make this muffin recipe with all-purpose flour?

Similar to replacing the oat flour with another gluten-free flour, this unfortunately won’t work with another type of flour. Instead, try one of my recipes made with all-purpose flour such as these Vegan Chocolate Chip Muffins, these Vegan Cranberry Orange Muffins, or these Vegan Banana Muffins.

Enjoy! If you make this recipe and decide to share it on Facebook or Instagram, don’t forget to tag me @FromMyBowl + #FromMyBowl! I would also love it if you could leave a comment below with a recipe rating! Thank you for the support 😊

Healthy Pumpkin Muffins (Gluten-Free)

4.88 from 32 votes
Prep Time 15 minutes
Cook Time 30 minutes
Total Time 45 minutes
Servings 12 muffins
Fluffy and moist, these Gluten-Free Pumpkin Muffins are the perfect pumpkin-filled treat! They're healthy enough breakfast, delicious enough for dessert, and packed with cozy fall flavors. Vegan, Gluten-free, Oil-Free, Refined-sugar free and Nut-free options.



  • Prep: Preheat the oven to 350F and grease or line a 12-muffin tin with paper liners. Blend the oats into a fine flour, if you haven’t done so already.
  • Mix the batter: Mix the pumpkin puree, milk, coconut sugar, nut butter, vanilla, and lemon juice together in a large bowl until a thick, even consistency forms. Add the blended oat flour, baking powder, baking soda, pumpkin pie spice, and salt to the bowl; mix well. Fold 3/4 cup of the walnuts or chocolate chips into the batter until evenly distributed.
  • Bake: Fill each muffin liner with ~1/2 cup of batter. Sprinkle the remaining 1/4 cup of nuts or chocolate over the muffin tops. Bake in the middle rack of the oven for 30 to 32 minutes, until fluffy and golden. Remove from the oven and let sit in the tin for 5 minutes before transferring to a baking rack. Let cool completely.
  • Storage: These muffins will keep at room temperature for up to 5 days, or can be frozen for up to one month.

Recipe Notes

  • Substitutions: Brown sugar can be replaced with coconut sugar or another granulated sweetener. You can use any nut or seed butter for this recipe, though I prefer almond butter or peanut butter. I have not tested this recipe with any other flours.
  • Oat Flour: To make oat flour, add the oats to a high-speed blender and process for 45 to 60 seconds, until a fine, fluffy flour forms.
  • Pumpkin Pie Spice: You can use a store-bought blend for this recipe, or make your own!


Calories: 237kcalCarbohydrates: 33gProtein: 5gFat: 11gSaturated Fat: 1gPolyunsaturated Fat: 3gMonounsaturated Fat: 6gSodium: 311mgPotassium: 269mgFiber: 4gSugar: 16gVitamin A: 5966IUVitamin C: 4mgCalcium: 145mgIron: 2mg
Keyword: gluten free pumpkin muffins, healthy pumpkin muffins, oat flour pumpkin muffins, oil free pumpkin muffins, one bowl pumpkin muffins, pumpkin spice muffins, vegan pumpkin muffins
Course: Breakfast
Method: Oven
Cuisine: American

About the Author

Hey there, I’m Caitlin! I make easy-to-follow, wholesome, and budget-friendly vegan recipes that are mostly gluten-free and refined sugar-free. I’m also an avid yogi, love the great outdoors, am chocolate-obsessed, and enjoy eating almond butter straight off of the spoon.

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  1. 5 stars
    One of my favorite recipes. I use brown sugar instead of coconut sugar and only about 3/4 cup.

    But please update the instructions! It lists baking soda in the ingredients but skips telling people to add it in the directions. Otherwise they won’t rise properly. Thanks

  2. 5 stars
    I have made these too many times to count. I start making them in the fall and continue to make them all winter. Our favorite muffins.

  3. 4 stars
    These are great muffins! Delicious! I would love to see the nutritional facts added to your recipes. This would be super helpful! Thank you!

  4. 5 stars
    Super delicious and a wonderful replacement for a pumpkin bar recipe I’d veganized myself. This is much more whole-foody and can be served to everyone so that’s a major plus!

    They also work perfectly in a mini muffin tin if anyone wanted to know! Reduced the time and they were delectably bite-sized!

  5. 5 stars
    I’ve been wanting to make these muffins forever and I finally did… and boy am I so happy! Most gf/vegan muffins are super gummy on the inside but these ones came out super fluffy and light. I added the walnuts, vegan chocolate chips and then pumpkin seeds on top and it’s just so bomb. The recipe made about 15 muffins for me and in the oven for 35 mins. Gonna make these every weekend!

  6. 5 stars
    The best vegan muffins I have ever made!! Plus an incredible bonus that they were made with blended oats instead of flour. I will 100% be trying out some more muffins varieties from your site 🙂

  7. 5 stars
    This recipe is amazing! Thank you!

    How would you go about doubling this recipe? Also how would cooking times and oven temp change?

    Thank you,
    Jenna C

    1. If you have two 12-muffin tins then all you need to do is quickly fill each tin and bake for roughly the same amount of time and at the same temperature. Use a toothpick to test if the centers are done at the normal time. If they need longer, add another 5 minutes.

  8. 5 stars
    Super tasty with a satisfying dense texture! I skipped the chocolate chips and used monk sugar instead of coconut sugar. sprinkled with pumpkins seeds instead of nuts. One of my fav recipes! While family loves them-thank you! All your recipe all seem to work and taste great! Wish u would whip up a delicious gluten-free rhubarb muffin recipe 🙂

  9. Hey Caitlin, if we are using a smaller muffin tray of 12 would it be the same amount of time and also filled to the middle??

    Thank you!!

    1. Filling to about half or a hair over half should still apply. As for cook time, it may need to be slightly shorter. I would check it at about the 20 minute mark, doing the toothpick test, and gauge it from there.

  10. 4 stars
    I accidentally made a flax egg thinking that it was needed and threw it in there anyways, the pumpkin muffins turned out great as far as the texture and consistency but I found mine not to have very much flavor wanting to add additional items in next time! I think it’s a great base for any flavor muffin really because I didn’t taste the pumpkin very much.

  11. 5 stars
    These. Are. Amazing. I’m so obsessed, and I will be making them every Sunday for snacking and breakfasts throughout the week!

  12. 5 stars
    I made these in the beginning of October and loved them! People on my dorm floor loved them too! I made them a second time for a vegan thanksgiving and not a single one was left over. The recipe makes 18 small muffins.

  13. 5 stars
    I made these yesterday and they are a hit! I didn’t have any ground ginger (like I thought I did) so my homemade pumpkin spice was made of 2 teaspoons cinnamon, 1/2 teaspoon ground nutmeg, and 1/4 teaspoon of ground cloves. I also ended up cooking my muffins (and the pan of extra batter I had leftover in a pan for about 40-45 minutes. I stuck a toothpick in the pan after 30 and 35 minutes and it came out sticky –– and while it was still sorta sticky after 45 minutes when the muffins cool, the goo dries and the muffins don’t taste undercooked. I thought maybe all that info might help others. MORE VEGAN & GLUTEN FREE RECIPES PLEASE!

    1. It’s true, a lot of vegan baked goods can seem a little gooey but when they cool down they’re totally normal! Thanks!

  14. 5 stars
    These these are phenomenal! As someone who has to eat gluten free, this is a great trick to just use oats I normally have on hand. I also had extra batter so I put it in a small pan and it kinda made pumpkin bars which worked well! The rise was good, but I did work quickly when I saw the vinegar reacting. Thanks for posting this recipe!!

  15. 5 stars
    These are soooooo yummy!!! I’m obsessed with this recipe, definitely a new fall go to! I made them with tahini, which worked great. Going to use almond butter next time and see the difference. Thanks for a great recipe!

  16. is this recipe supposed to make 12 jumbo sized muffins or regular? I just made it in a regular muffin tin and ended up with a lot of extra batter.

    1. Hey! It should be 12 regular sized muffins, we fill pretty high up as well (there should be a picture on the blog). Did you fill yours up as high?

  17. 5 stars
    These muffins are amazing! Best vegan muffin recipe that I’ve tried so far! I substituted the oat flour for whole wheat flour and they turned out just fine. I did also have to bake these muffins for about 40 minutes, but overall, DELICIOUS!

  18. 5 stars
    made these twice now and i love them so much! the first time i made them i was a little short on oats so i subbed with a little bit of cassava flour and they worked great. oat flour is much cheaper though if you make it yourself, so the second time i made it exact and they are pretty much the same! i keep them in the freezer and just heat up one when I want! excited for a pumpkin cookie recipe 😉

  19. I made these when you first posted them at the same time I made your banana bread. So I froze the muffins and ate the banana bread first. These muffins are amazing!!! I used less sugar and they are perfectly sweet, fluffy, pumpkiny, everything is great about them!! Thank you for this recipe, as always you are amazing!