Gluten-Free Pumpkin Muffins

5 from 49 votes
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These sweet and spicy Gluten-Free Pumpkin Muffins are perfectly tender and loaded with pumpkin flavor. Made with wholesome ingredients and no refined sugar, these muffins are a wonderful fall treat for the whole family.

A plate of gluten-free pumpkin muffins with a bite taken out of one.

Gluten Free Pumpkin Muffins Recipe

Pumpkin muffins are the ideal fall baking project, and when they are gluten-free, they’re even better! When the breeze turns brisk there’s nothing I like better than pouring myself a hot mug of coffee or tea, putting on a warm sweater, and indulging in a seasonal breakfast treat. Pumpkin muffins are exactly what you want when the calendar ticks over into autumn.

These gluten-free pumpkin muffins are loaded with cozy spices and mellow pumpkin puree and are lightly sweetened with the dark richness of coconut sugar plus a little maple syrup. A homemade pumpkin pie spice adds flavor depth and a little heat. The crumb is so tender and moist you’ll hardly notice this is a gluten-free recipe. And, it’s so easy to make dairy-free if needed (see my tips below).

This one is definitely a keeper! It’s a two-bowl, easy-to-throw-together batter that’s sure to be a favorite throughout fall and beyond. And, it only takes 10 minutes to prep so you’ll have a bowl of soft, lightly steaming muffins on the table in less than half an hour.

A wire rack of gluten-free pumpkin muffins.

Why You’ll Love These Healthy Pumpkin Muffins

I love a muffin for breakfast, and fragrant, tender pumpkin muffins that are actually good for me are one of my favorites. Here’s why you’ll love these gluten-free pumpkin muffins:

  • Full of fall flavors. Crisp fall mornings absolutely need a spice mix, and you’ll find a wonderful blend of pumpkin pie spice plus more ginger and cinnamon in these muffins.
  • So cozy. I think these muffins are so cozy! Is it the spices? The mellow pumpkin and just sweet enough maple syrup note? All of the above? These gluten-free pumpkin muffins are just right for fall.
  • Healthy. There are so many healthy aspects to this recipe, from the heart-healthy avocado oil to the lack of granulated sugar, making these a good breakfast choice.
  • Refined sugar-free. I love a recipe that doesn’t call for a ton of granulated sugar. The sweetness in these healthy pumpkin muffins comes from maple syrup and coconut sugar, both of which are unrefined sweeteners.
  • Gluten-free. This pumpkin muffin recipe is easily adapted to be gluten-free when you use gluten-free all-purpose flour in place of wheat flour. The rest of the ingredients needed are naturally gluten-free.
A hand holds a pumpkin muffins.

What You’ll Need

Here’s a rundown of the ingredients you’ll need to make these gluten-free pumpkin muffins. Don’t forget to scroll down to the recipe card at the end of this post for the full ingredient amounts.

  • Gluten-Free All-Purpose Flour: I like to use Bob’s Red Mill Gluten-Free 1:1 All-Purpose Flour, but you can use your preferred blend of gluten-free all-purpose flour.
  • Baking Powder: To help the muffins rise.
  • Pumpkin Pie Spice: You can make your own pumpkin pie spice or use store-bought.
  • Sea Salt: You can substitute it with table salt.
  • Ground Spices: Cinnamon and ginger. Ground cinnamon and ginger add a little more spice to this pumpkin recipe.
  • Canned Pumpkin Puree: Be sure to purchase 100% pumpkin puree instead of pumpkin pie filling. Homemade pumpkin puree can also be used.
  • Avocado Oil: Any neutral-flavored liquid cooking oil will work. You can also use melted butter or melted coconut oil (measure after it’s been melted).
  • Maple Syrup: The flavor of pure maple syrup pairs so well with pumpkin, but you can substitute granulated sugar or brown sugar.
  • Coconut Sugar: Coconut sugar is refined sugar-free and has a wonderful toasty, caramel-ly flavor. You can substitute brown sugar for coconut sugar.
  • Eggs: Eggs help give the batter structure.
  • Milk: I like to use whole milk in this recipe for richness.
  • Vanilla Extract: Pure vanilla extract will give the best flavor.
  • Turbinado Sugar: Turbinado sugar is a coarse sugar that creates a beautiful, crunchy sugar topping. This ingredient is optional and can be omitted if you want to keep this recipe refined sugar-free.
Ingredients for gluten-free pumpkin muffins: gluten-free flour, salt, vanilla, eggs, pumpkin puree, milk, maple syrup, coconut sugar.

How to Make Gluten Free Pumpkin Muffins

You need just two bowls for this recipe and it comes together so easily. Here’s my method for making gluten-free pumpkin muffins:

  • Heat the oven. Preheat the oven to 425℉.
  • Combine the dry ingredients. In a bowl, combine the dry ingredients (except the coconut sugar) and whisk together until all ingredients are evenly dispersed.
  • Combine the wet ingredients. In a separate large mixing bowl, combine the remaining ingredients and whisk together until the pumpkin is fully incorporated and there are no lumps.
  • Combine the wet and dry ingredients. Pour the dry ingredients into the bowl with the wet ingredients and stir until the batter is smooth and lump free.
  • Transfer to the muffin tin. Line a muffin tin with silicone muffin liners (do not use paper liners for this recipe because they will stick to the muffins). Divide the batter between the muffin wells using a 2-ounce scoop or spoon. If using, sprinkle the muffins with turbinado sugar (you do not have to use a full ¼ cup, just enough to give them a nice crunchy sugar topping).
  • Bake the muffins. Place the muffins in the preheated oven and set a timer for 5 minutes. After 5 minutes, reduce the temperature to 350 F (leaving the muffins in the oven) and bake for another 15-17 minutes or until the muffins can be poked with a toothpick that comes out clean.
  • Cool. Remove the muffins from the oven and allow them to cool in the tin for at least 5 minutes. Once cooled, remove from the tin and store uncovered at room temperature until fully cooled.

Tips for Success

This is a lovely, simple recipe for pumpkin muffins. Here are a few tips to ensure success:

  • Reduce the sugar slightly. If you prefer less sweet muffins, you can reduce the coconut sugar to ⅓ cup and omit the turbinado sugar sprinkled on top. 
  • Don’t open the oven door when you lower the oven temperature. When changing the temperature from 425℉ to 350℉, there is no need to open the oven door or remove the muffins from the oven. Keep the muffins in the oven and allow them to continue to cook.
  • Cooking time will depend on your muffin tin. Muffins in tins that are dark grey or black will cook faster than muffins in lighter-colored tins. 
  • Let the muffins fully cool after they bake. Allow the muffins to cool fully before placing them in an airtight container or Ziploc bag.
  • Make them dairy-free. Use your favorite non-dairy milk in this recipe to make the pumpkin muffins dairy-free.
  • Use homemade pumpkin puree. You can make your own pumpkin puree from a pumpkin: cook a peeled, chopped pumpkin (with its seeds removed) in water until fork-tender, then drain it and puree it in a blender or food processor. You’ll need 2 cups of pumpkin puree to make these muffins.
  • Add chocolate chips. I admit it – I will sometimes throw in a cup of semi-sweet chocolate chips or mini chocolate chips into the batter. Pumpkin and chocolate go so well together.
A hand holds two halves of a pumpkin muffin.

Can I Make These Pumpkin Muffins Vegan?

Yes! I tested this recipe using “flax eggs” in place of eggs and almond milk instead of dairy milk. Note that you can use a non-dairy milk of your choice. If you use flax eggs, the muffins will be a bit denser and may take longer to bake. If you try another type of egg replacement let us know how it went in the comments below!

Here’s how to make flax eggs: To make 2 “flax eggs”, combine 2 tablespoons of ground flax seeds with 5 tablespoons of warm water and stir together. Let the mixture sit for a few minutes until it thickens, then stir the “eggs” into the wet ingredients where the eggs are added in the recipe (step 3).

Gluten-free pumpkin muffins on a plate, one has a bite taken out from it.

Common Questions

Are these gluten-free pumpkin muffins healthy?

These gluten-free pumpkin muffins are made from wholesome ingredients and are refined sugar-free. We do use refined gluten-free flour, but the muffins contain a hearty serving of nutrient and fiber-rich pumpkin puree and nothing artificial making them a healthier option than most conventional muffins. Each muffin contains 4 grams of fiber and 4 grams of protein!

What can I use if I don’t have silicone muffin liners?

Paper muffin liners will not work for this recipe because the muffins will stick to the paper. If you do not have silicone muffin liners, grease the muffin tin with coconut oil or cooking spray and scoop the batter directly into the wells of the muffin tin. 

A wire rack of gluten-free pumpkin muffins.

Proper Storage

Allow the muffins to cool on the counter overnight and then place them in a Ziploc bag or airtight container and store at room temperature for 4-5 days. Allowing the muffins to cool overnight is helpful because the pumpkin adds a significant amount of moisture and if they are even slightly warm when put in an airtight bag, they will become soggy. 

Can I Freeze Homemade Pumpkin Muffins?

Yes! These pumpkin muffins freeze well and can be stored in the freezer for up to 1 month. Remove the muffins from the freezer and defrost them in the fridge before you heat or eat them. These muffins are best reheated using a dry heat method like the oven or toaster oven instead of the microwave because freezing and thawing can make them more moist.

Gluten-free pumpkin muffins are stacked on top of each other.

Where to Find Silicone Muffin Liners

These muffin or cupcake liners are available in many stores, including kitchen stores, Target, and IKEA. You can also get an inexpensive and colorful set on Amazon.

Gluten-free pumpkin muffins on a plate, one has a bite taken out from it.
5 from 49 votes

Gluten-Free Pumpkin Muffins

These sweet and spicy Gluten-Free Pumpkin Muffins are perfectly tender and loaded with pumpkin flavor. Made with wholesome ingredients and no refined sugar, these muffins are a wonderful fall treat for the whole family.
Prep: 10 minutes
Cook: 20 minutes
Total: 30 minutes
Servings: 12 muffins

Ingredients

  • 2 cups/275 grams gluten-free 1:1 all-purpose flour (I used Bob's Red Mill), spooned and leveled
  • 2 teaspoons baking powder
  • 2 teaspoons pumpkin pie spice
  • 1 teaspoon sea salt
  • 1 teaspoon ground cinnamon
  • ¼ teaspoon ground ginger
  • 1 ½ cups/360 grams canned pumpkin puree (not pumpkin pie filling)
  • ½ cup/120 ml avocado oil
  • ½ cup/120 ml maple syrup
  • ½ cup/90 grams coconut sugar
  • 2 large eggs
  • ¼ cup/60 ml milk or non-dairy milk
  • 1 teaspoon vanilla extract
  • ¼ cup turbinado sugar, for topping (optional)

Instructions

  • Preheat the oven to 425℉.
  • In a bowl, combine the dry ingredients (except the coconut sugar) and whisk together until all ingredients are evenly dispersed. Line a muffin tin with silicone muffin liners (do not use paper liners for this recipe because they will stick to the muffins).
  • In a separate large mixing bowl, combine the remaining ingredients and whisk together until the pumpkin is fully incorporated and there are no lumps.
  • Pour the dry ingredients into the bowl with the wet ingredients and stir until the batter is smooth and lump free.
  • Divide the batter between the muffin wells using a 2-ounce scoop or spoon. If using, sprinkle the muffins with turbinado sugar (you do not have to use a full ¼ cup, just enough to give them a nice crunchy sugar topping).
  • Place the muffins in the preheated oven and set a timer for 5 minutes. After 5 minutes, reduce the temperature to 350℉ (leaving the muffins in the oven) and bake for another 15-17 minutes or until the muffins can be poked with a toothpick that comes out clean.
  • Remove the muffins from the oven and allow them to cool in the tin for at least 5 minutes. Once cooled, remove from the tin and store uncovered at room temperature until fully cooled.
Nutrition Facts
Gluten-Free Pumpkin Muffins
Amount Per Serving (1 muffin)
Calories 250 Calories from Fat 99
% Daily Value*
Fat 11g17%
Saturated Fat 1g5%
Trans Fat 0.01g
Polyunsaturated Fat 2g
Monounsaturated Fat 7g
Cholesterol 31mg10%
Sodium 225mg9%
Potassium 184mg5%
Carbohydrates 37g12%
Fiber 3g12%
Sugar 19g21%
Protein 4g8%
Vitamin A 4818IU96%
Vitamin C 1mg1%
Calcium 80mg8%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.
Disclaimers: Please discuss your individual dietary needs (i.e. gluten free) with a physician. Even when not specified, be sure to verify all ingredients are gluten free, if needed, by reading labels on all packaging and/or confirming with the manufacturer this varies by brand and can change at any time. Nutrition information shown is an estimate and not guaranteed to be accurate.

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1 Comment
  1. Sarah

    5 stars
    Really great recipe. Easy and delicious! I made a loaf with half of the batter and baked for 40-45 min. So perfectly perfect! I’ll be making this again. Often.

4.98 from 49 votes (48 ratings without comment)

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