Healthy Gluten-Free Pumpkin Muffins

GFGluten FreeNFNut FreeOFOil FreeSFRefined Sugar FreeVVegan
4.87 from 30 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)

4.87 from 30 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
    I have made this recipe several times to rave reviews! Those that ask, I send them the link for the recipe. Thank you.

  2. I was looking for a copycat for the TJ GF pumpkin muffins…THESE ARE BETTER than the TJ ones!! They are AMAZING and super easy to make. The first time, I used coconut sugar instead of brown sugar. The second time, I used coconut sugar and just half the amount and used maple syrup for the other half. Thank you for sharing the recipe!

  3. 5 stars
    I never comment on recipes, but I have made these muffins half a dozen times by now. They are excellent and they freeze great! I bring them almost every day in my lunch and they are perfectly thawed by lunchtime. I love that they are not overly sweet and the texture is incredible. I like to add cranberries in addition to the nuts and dark chocolate chips. Amazing.

  4. 5 stars
    We are making these on repeat in my family! Thank you for this recipe! We use dairy, so I have subbed melted butter for the nut butter and it’s very good!

    1. If you are using store-bought oat flour I would recommend going by the metric (g) measurements for the oats as that will yield the most accurate results 🙂

  5. 5 stars
    Love this recipe. The texture of the muffins is great and when they were warm they had a slight peanut butter taste (yum!). I used pecans since that was in the ingredient list and I didn’t think I had any walnuts. Next time, the chocolate chip will be added and they are going to be shared at a retreat.