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Meal Type » Gluten Free Snack Recipes » Gluten Free Pumpkin Muffins

Gluten Free Pumpkin Muffins

Claire Cary

By

Claire Cary

5 from 39 votes
Updated: November 1, 2024
Jump to Recipe

These gluten free pumpkin muffins are the perfect Fall recipe. They’re filled with chocolate chips and topped with cinnamon streusel. They’re light, fluffy and so easy to make!

two gluten free pumpkin muffins stacked on each other with chocolate chips

It’s officially pumpkin season and I for one am so excited. Pumpkin bread, pumpkin cookies, pumpkin pie and these new gluten free pumpkin muffins!

I couldn’t decide between doing chocolate chips or a cinnamon streusel topping, so I opted for both! These muffins have a generous amount of pumpkin for a very soft and tender texture, plus plenty of spice for tons of flavor. They’re perfect for a quick snack or dessert and I promise you’d never tell they’re both gluten and dairy free.

These muffins are made with gluten free all purpose flour and good old sugar, but if you’re looking for a healthy muffin recipe with almond flour, try my sweet potato muffins instead! If you’re really in the Fall baking spirit, my gluten free pumpkin cinnamon rolls and gluten free pumpkin pie always hit the spot.

Tips before we get started!

  • I love these with both the streusel and chocolate chips, but you can opt to do just one or keep the muffins plain! The base recipe has tons of flavor as is.
  • Be sure to use pure pumpkin puree, not pumpkin pie filling.
  • For extra tall muffins, you can bake in two muffin tins and just bake 6 at a time, leaving space between each muffin. This allows the air to circulate better and creates taller muffins.
    ingredients in bowls with labels

    How to make gluten free pumpkin muffins

    WHISK WET. In a large mixing bowl, whisk together all wet ingredients until smooth.

    WHISK DRY. Whisk in the dry ingredients, making sure to spoon and level the flour. Fold in the chocolate chips. Scoop the batter into a muffin tray, filling each to the top to ensure nice round muffin tops.

    MAKE STREUSEL. In a small dish, combine the sugar, flour and pumpkin pie spice. Cut in the butter or coconut oil with a fork until crumbly.

    BAKE. Use your fingers to sprinkle the streusel on top of the muffins. Bake for 28-32 minutes or until a toothpick comes out clean.

    SERVE. Let cool for about 15 minutes in the tray, then remove and transfer to a wire rack to finish cooling and enjoy!

    two images showing how to make the recipe

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    Can I make them vegan?

    You can try subbing the eggs for an egg substitute like flax eggs or a store bought egg replacer, but they likely won’t rise as well. The eggs are important here for a fluffy texture and ensuring a nice rise, so I recommend sticking with the recipe as written for best results!

    Vegan and gluten free baking is very tricky, so it’s usually best to opt for a recipe that is already developed to be that way.

    pumpkin muffins in a muffin tray before going in the oven

    Ingredient swaps

    PUMPKIN. You need pure pumpkin puree for this recipe and it cannot be subbed with pumpkin pie filling. Pumpkin pie filling already contains all the spices, sugar and other ingredients in pumpkin pie, so be sure you’re using just plain pumpkin puree for these muffins. You will need just shy of one 15 ounce can.

    FLOUR. This recipe calls for gluten free all purpose baking flour, which you cannot sub for almond, coconut, oat or another type of flour. You can use regular all purpose flour (non gluten free), but please do not try using another gluten free flour such as almond, oat etc. I like the Bob’s Red Mill 1:1 Baking Flour, just make sure whatever you use has xanthan gum!

    SUGAR. You can sub the light brown sugar for coconut sugar, but I don’t recommend subbing the white sugar for coconut sugar. The muffins will be a very dark color and they may not rise as well. You can always try my healthy sweet potato muffins if you want a lower sugar option!

    up close of one muffin with a bite taken out to show texture

    How to store and freeze

    Once prepared, these gluten free muffins will keep for about 3 days at room temperature, or 5 days in the fridge. They can get a bit soggy if put in an air tight container because of the pumpkin, so I suggest leaving them in a container with the lid slightly ajar or covered loosely with foil.

    You can freeze these gluten free pumpkin muffins after they bake. Be sure to let them cool completely, then transfer to a freezer safe bag and freeze for up to one month. Let them defrost in the fridge overnight, then warm up in the oven or microwave.

    gluten free pumpkin muffins with streusel and glaze on top

    Try these snack recipes next!

    • Matcha Muffins
    • Almond Flour Blueberry Muffins
    • Gluten Free Zucchini Muffins
    • Gluten Free Pumpkin Bread
    • Protein Muffins
    • Mini Chocolate Chip Muffins

    Lastly, if you want more recipes straight to your inbox, be sure to subscribe to my email list. As always, tag me on instagram if you make this recipe so I can see your creation!

    5 from 39 votes

    Gluten Free Pumpkin Muffins

    by: claire cary

    These gluten free pumpkin muffins are the perfect Fall recipe. They’re filled with chocolate chips and topped with cinnamon streusel. They’re light, fluffy and so easy to make!
    / /
    Prep: 15 minutes mins
    Cook: 30 minutes mins
    Total: 45 minutes mins
    12

    Ingredients

    Wet

    • 2 large eggs
    • 6 tablespoons melted butter or coconut oil
    • 1 ½ cups pure pumpkin puree
    • ⅔ cup white sugar
    • ½ cup light brown sugar
    • 2 teaspoons vanilla
    • 1 teaspoon apple cider vinegar

    Dry

    • 1 ¾ cup gluten free all purpose baking flour
    • 1 ½ teaspoons baking powder
    • ½ teaspoon baking soda
    • ½ teaspoon salt
    • ½ teaspoon cinnamon
    • 2 ¾ teaspoons pumpkin pie spice
    • ½ cup chocolate chips

    Streusel

    • 4 tablespoons brown sugar
    • 4 tablespoons gluten free all purpose flour
    • 2 tablespoons butter or coconut oil softened
    • ¼ teaspoon pumpkin pie spice
    US Customary – Metric

    Instructions

    • Preheat the oven to 350 degrees Fahrenheit. Line a muffin tin with 12 liners and set aside.
    • In a large mixing bowl, whisk together all wet ingredients until smooth.
    • Whisk in the dry ingredients, making sure to spoon and level the flour.
    • Fold in the chocolate chips.
    • Scoop the batter into a muffin tray, filling each to the top to ensure nice round muffin tops.
    • In a small dish, combine the sugar, flour and pumpkin pie spice. Cut in the butter or coconut oil with a fork until crumbly.
    • Use your fingers to sprinkle the streusel on top of the muffins. Bake for 28-32 minutes or until a toothpick comes out clean.
    • Let cool for about 15 minutes in the tray, then remove and transfer to a wire rack to finish cooling.

    Notes

    You can sub the light brown sugar for coconut sugar, but I don’t recommend subbing the white sugar for coconut sugar. The muffins will be a very dark color and they may not rise as well. You can always try my healthy sweet potato muffins if you want a lower sugar option!
    This recipe calls for gluten free all purpose flour, which you cannot sub for almond, coconut, oat or another type of flour. You can use regular AP flour (non gluten free), but please do not try using another gluten free flour. I like the Bob’s Red Mill 1:1 Baking Flour, just make sure whatever you use has xanthan gum!
    Serving: 1muffin / Calories: 282kcal / Carbohydrates: 42g / Protein: 4g / Fat: 10g / Saturated Fat: 7g / Fiber: 3g / Sugar: 24g

    Did you make this?

    Mention @eatwithclarity or tag #eatwithclarity!

    5 from 39 votes (10 ratings without comment)

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    Recipe Rating




    Comments

    1. Brooke
      October 5, 2026

      These are the best gluten free muffins I’ve ever made.5 stars

      Reply
      1. Claire Cary
        October 6, 2026

        Thank you, Brooke!

        Reply
    «Older Comments
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    claire cary

    Welcome,
    I’m Claire

    Eat With Clarity is a place for gluten free recipes that are just as good as the real thing. With plenty of vegan, vegetarian and paleo options, there is something here for everyone!


    Read Claire’s Story

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