Healthy Gluten-Free Pumpkin Muffins

GFGluten FreeNFNut FreeOFOil FreeSFRefined Sugar FreeVVegan
4.88 from 31 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 31 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. Oh my goodness Caitlin these are seriously the best pumpkin muffins I have ever made!! I chose to use mini chocolate chips as my add-in. I had already had them in the oven when I realized I forgot the lemon juice I’m just curious if you could tell me what the purpose is of that and if I should try to include it next time. They seemed to have turned out really well. Do you by any chance have a pumpkin cookie recipe that’s similar to this? The flavor is just amazing.

    1. Thanks so much, glad you enjoyed them! The lemon juice would react with the baking soda/powder to help create more of a leavening. No pumpkin cookies.. yet!

    1. We haven’t tested it with an alternate flour, so not sure how that particular one would work out. But if you give it a try let us know how it goes!

  2. 5 stars
    Love all your recipes!! I’m making these muffins today. Was wondering though, you have baking soda as an ingredient yet there’s no mention of it in the directions. Is it needed?

  3. 5 stars
    I can ALWAYS count on Caitlin to come through with recipes that are easy, quick, healthy, and require ingredients that I actually have all without any sacrifice to the flavor. These muffins are fantastic and a must make this fall (or any season really).

  4. 5 stars
    I made these with whole wheat flour and brown sugar instead of oat flour and coconut sugar and they turned out perfectly! Great recipe, as always.

  5. 5 stars
    These are delicious! I made some yesterday and used pumpkin seeds, cinnamon chips and butterscotch chips because I like to indulge. However, the rise they had didn’t last after baking. I’m not sure why. Doesn’t matter, they are still heavenly and I will be making them again!

    1. So happy you liked them! If you had issues with your rising, it may be the reaction between apple cider and the baking soda. Once you get to the step where those ingredients come into contact moving quickly would help get them in the oven before the reaction ends.

  6. Does the recipe need 2.5 cups of oat four or 2.5 cups oats ground into flour? I have a bunch of oat flour already made but don’t know exactly how much oats I used. Can’t wait to make these!

    1. 2.5 cups of oats, blended into a flour. If you already have oat flour you can use a food scale and go by weight instead 🙂

  7. 4 stars
    I made these! PROS: phenomenal flavor, not too sweet, beautiful rise to the muffins, love the use of an entire can of pumpkin. CON: texture a little gummy in the interior. Thank you, Caitlin!

  8. I juste made the muffin, they tasted amazing. But, after 30 minutes in the oven, the center of the muffin were still very undercooked in the middle. I cook them almost 10 minutes extra and still undercooked. I still enjoyed them but any tips for the cooking time?

    1. It could have to do with the altitude of where you live, the freshness of your baking powder, or a slight difference in measuring cup size. Also, be sure to wait until the muffins are completely cooled, otherwise they will be sticky in the center!

    2. 4 stars
      These are super easy and yummy. But mine were still really squishy in the center. I’m a sugar addict so I ended up ripping these with a little maple syrup but I think peanut butter would be yummy on top too!! This was my first time trying one of your recipes but I watch your videos every week!! Thanks so much for the inspiration (:

    1. Hmm.. that would take some adjusting to get a proper cookie, most likely just end up making a new recipe at that rate. We’ll see what we can do!

  9. Just made them! Waiting to cool off so I can try.
    I added in the baking soda with the dry ingredients, just wanted to let you know it isn’t in the actual directions for the recipe.

    1. If you’re making your own puree, for sure you can use that! Your pumpkin consistency should not be liquidy, it should stay rounded in a mound when you scoop it with a spoon.

  10. My question is, do you grind the oats first and then measure? Looking forward to warm oven in the cool evening and luscious scent when they’re baking!

    1. I measure the oats first and then grind, though it doesn’t really make a difference as long as you use the same weight!

    1. Haven’t tested it with flour alternatives (keeping it GF). Do you have a preference on a certain flour type?

  11. 5 stars
    Love your recipes!!! This has helped me and my dad to eat healthier. And also do we have to use oat flour can we use a different one?

  12. Hey Caitlin – These look awesome!! I have all the ingredients just need the pumpkin puree. Think I’ll go get the can and make these this afternoon. Thanks for the recipe. My son gets home early from school today. You are ahhhmazing! Love all your videos, your blog everything. Been following you for a long time. I’m a Realtor in Texas. Congrats on your new home little belated but I’m sure you love it! I saw your video the other day about your being down happens to all of us. You are doing great keep it up. Lots of love from Houston:)!

    1. That’s so kind, thank you so much! I hope you enjoy the muffins and all the future fall recipes to come!

  13. Would it change the recipe, other than making it less sweet to do less coconut sugar? Trying to avoid lots of sugar. Sound delish, can’t wait to try!

    1. You should be able to add less sugar without any issue, so long as the amount you reduce isn’t a lot, otherwise you may need to compensate with more oat flour to compensate.

    2. Did you reduce the sugar in the recipe? I would be curious to know your result. Im unsure how much I can leave out. Im sure 1/4 c but 1/2c ??

  14. 5 stars
    That sounds great! I loved your pumpkin bread last year and am sure to try these 🙂
    And I love, that you added grams/ml to the recipe!