There are two things that always happen when these come out of the oven. The kitchen smells like October. And then they disappear.

These gluten free pumpkin muffins use 1:1 gluten-free flour, which means they bake up like the real thing.

Tall tops, soft centers, warm with pumpkin pie spice, and if you go the chocolate chip route, melty pockets of chocolate in every bite. This is the fall breakfast your mornings have been missing!

Why These Gluten-Free Pumpkin Muffins Are a Fall Must-Bake

bowl of turkey teriyaki vegetables and rice on a counter and then a close up of ground turkey teriyaki rice bowl
  • Spiced and pumpkin-forward. The right ratio of pumpkin pie spice and real pumpkin puree means these taste like fall in every bite, not like flour with a little orange color.
  • Tall tops, soft centers, every time. A two-temperature baking trick (425°F for five minutes, then 350°F) gives you the bakery-style rise. The center stays soft. The top goes golden. More on this below.
  • GF Pumpkin chocolate chip muffins. add chocolate chips for melty pools of chocolate and pumpkin. My kids love them this way!
  • One bowl, 10 minutes of active time. Whisk, fold, scoop. Done.
  • Swappable for your table. Dairy-free, egg-free, refined sugar-free — the notes section covers all of it.
  • Freezer-friendly. Make a double batch. Wrap them individually. You’ll thank yourself in November.

Love gluten free muffins? Try healthy banana muffins or gluten-free morning glory muffins next! Use gluten-free flour in these mini chocolate chip muffins!

a batch of gluten free pumpkin muffins with chocolate chips on a cooling rack with bowls of pumpkine puree and chocolate chips visible around them.

Reader Reviews

⭐️⭐️⭐️⭐️⭐️ “Brought these to work and everyone loved them! They are so moist, very tasty, and the perfect size!” — Becca

⭐️⭐️⭐️⭐️⭐️ “Exceeded all expectations for gluten intolerant and tolerant family members! Delicious! Thanks!” — Eileen

Love pumpkin treats? Try cinnamon swirl pumpkin bread, healthy pumpkin muffins, or healthy pumpkin coffee cake next.

Ingredients You’ll Need

labeled ingredients for gluten free pumpkin muffins on a counter.
  • Brown sugar + granulated sugar. The brown sugar is what keeps these moist and adds depth. Use coconut sugar 1:1 for a refined sugar-free version.
  • Pumpkin puree. 100% pure canned pumpkin only. Not pumpkin pie filling. Pie filling has added sugar and spices that will throw off the whole recipe.
  • Unsalted butter. Melt it first and let it cool slightly before adding to the eggs. Hot butter can scramble them. Coconut oil or vegan butter works 1:1 for dairy-free.
  • 1:1 Gluten-Free Flour. Use a blend that already contains xanthan gum. I like Bob’s Red Mill 1:1 or King Arthur’s Measure for Measure. Do not substitute almond flour or coconut flour — the ratios are completely different and the recipe won’t work.
  • Baking powder + baking soda. Both. Don’t skip either. GF baked goods need all the lift they can get.
  • Pumpkin pie spice. Go up to 2.5 teaspoons if you want it more pronounced. The recipe notes have a homemade blend if you’re out.
  • Chocolate chips (optional, strongly recommended). Semi-sweet holds up best here. If you’re skipping them, a sprinkle of turbinado sugar on top before baking adds a crackly crust.
Jump to Recipe

How to Make Gluten-Free Pumpkin Muffins

A glass bowl filled with pumpkin pie filling mixture and a metal whisk—perfect for making gluten-free pumpkin muffins. In the upper left corner, a small bowl holds vibrant orange pumpkin puree.

Step 1. Wet ingredients: Whisk the wet ingredients in a large bowl until combined and smooth.

A glass bowl filled with flour, baking powder, and ground cinnamon for gluten-free pumpkin muffins, with a metal whisk resting on the right side of the bowl, ready for mixing.

Step 2. Dry ingredients: Whisk together the dry ingredients in a medium bowl.

A mixing bowl of pumpkin batter for gluten-free pumpkin muffins with chocolate chips being stirred in using a pink spatula. A small bowl of pumpkin puree sits in the background.

Step 3. Combine and rest: add the dry ingredients to the wet ingredients until just combined. Don’t over-mix. The batter will be thick. Let it rest for 10 minutes to let the flour absorb the moisture and to give the baking soda a jump start.

A muffin tin filled with unbaked gluten-free pumpkin muffins batter, each lined with a paper cup and topped with chocolate chips, sits on a light-colored countertop.

Step 4. Fill tins: Scoop the batter into muffin cups lined with paper liners. Fill each cup all the way full, nearly overflowing. Reserve a few chocolate chips for the tops.

A muffin pan filled with twelve freshly baked gluten-free pumpkin muffins, golden brown with chocolate chips scattered on top, sits on a light-colored surface.

Step 5. Bake: Bake at 425°F for 5 minutes, then reduce to 350°F without opening the oven door. Bake another 15 to 18 minutes until a toothpick comes out clean.

Molly’s Tips for Bakery-Style Muffins

The tall muffin top trick.

Start at 425°F for five minutes, then reduce to 350°F without opening the oven door. That initial blast of heat gets the muffins rising fast, before the center has time to set. That’s the difference between a flat top and a domed one.

The batter rest is just as important. Let it sit for 10 minutes before scooping. Gluten-free flour absorbs liquid differently than regular flour, and that rest is what gets the texture right. The batter will look thick and scoopable. That’s exactly right.

Fill the cups all the way full. Almost overflowing. It sounds like too much. It’s not. This is where the tall top comes from.

Want more texture on top? Turbinado sugar before baking gives a crackly, golden crust. Or borrow the streusel from this gluten-free coffee cake recipe.

I use these tips for all my muffin recipes, including pumpkin streusel muffins, chocolate chip oat muffins, and almond flour banana muffins.

Dietary Modifications (Dairy-Free Option)

Dairy-free: Swap butter for melted coconut oil or vegan butter, 1:1. Use dairy-free chocolate chips.

Egg-free: Use flax eggs (1 tablespoon flaxseed meal + 3 tablespoons water per egg, let sit five minutes before using).

Refined sugar-free: Use coconut sugar in place of brown sugar, same amount.

How to Freeze Muffins

Cool completely, wrap individually, and freeze in an airtight bag for up to two months. Thaw in the fridge overnight or microwave for 20 to 30 seconds.

It’s how I keep gluten-free morning glory muffins and healthy banana muffins stocked year round.

More Gluten-Free Pumpkin Recipes

Or check out all of my gluten-free muffin recipes!

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4.64 from 118 votes

Gluten-Free Pumpkin Muffins

Prep: 10 minutes
Cook: 25 minutes
Total: 35 minutes
Soft gluten free pumpkin muffins using 1:1 gluten-free flour gives you warm pumpkin spice and melty chocolate chips in every bite. The two-temperature baking trick gives you tall, bakery-style tops with soft centers every time.
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Molly Thompson

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Molly Thompson
Servings: 12 muffins

Ingredients

  • 2 large eggs
  • 3/4 cup light packed brown sugar packed, or coconut sugar
  • 1/4 cup granulated sugar
  • 1 cup pumpkin puree
  • 3/4 cup unsalted butter melted and slightly cooled
  • 1 teaspoon vanilla extract
  • 1 3/4 cups 1:1 gluten free flour I use Bob's Red Mill
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 2 teaspoons pumpkin pie spice
  • 1 cup semi-sweet chocolate chips
Standard – Metric

Instructions 

  • Preheat oven to 425°F. Line a 12 count muffin pan with liners and spray them nonstick cooking spray and set aside.
  • In a large mixing bowl, whisk the eggs, brown sugar, granulated sugar, pumpkin puree, melted butter and vanilla until combined.
    2 large eggs, 3/4 cup light packed brown sugar, 1/4 cup granulated sugar, 1 cup pumpkin puree, 3/4 cup unsalted butter, 1 teaspoon vanilla extract
  • In a medium bowl, whisk together the gluten-free flour, baking powder, baking soda, salt and pumpkin pie spice. Add the dry ingredients to the wet ingredients and gently whisk until just combined, being careful not to over mix. Add the chocolate chips, reserving a few for the tops of the muffins, and fold in gently. The batter will be thick. Let the batter rest for 10 minutes.
    1 3/4 cups 1:1 gluten free flour, 1 teaspoon baking powder, 1 teaspoon baking soda, 1/2 teaspoon salt, 2 teaspoons pumpkin pie spice, 1 cup semi-sweet chocolate chips
  • Scoop the muffin batter out of the bowl and fill each muffin tin all the way full, almost overflowing. Add the reserved chocolate chips to the top of the unbaked muffins.
  • Bake the muffins 5 minutes at 425°F then, keeping the muffins in the oven, reduce the oven temperature to 350°F. Bake for an additional 15-18 minutes, or until a toothpick inserted in the center comes out clean.
  • Remove the muffins from the oven and allow to cool in the pan for 5-10 minutes then transfer to a wire rack to cool completely. Store in an air tight container at room temperature for up to 5 days or in the freezer for up to 3 months.
Last step! If you make this, please leave a review letting us know how it was!

Notes

Pumpkin Puree. This is plain canned pumpkin, not pumpkin pie filling.
Homemade Pumpkin Spice. 1 teaspoon cinnamon, ½ teaspoon nutmeg, ¼ teaspoon cloves, ¼ teaspoon ground giner.
Dairy-Free. Use coconut oil or vegan butter instead of regular butter.
Egg-Free. Swap in flax eggs (1 Tbsp flaxseed meal + 3 Tbsp water per egg).
Refined Sugar-Free. Use coconut sugar instead of brown sugar.
Storage. Keep muffins in an airtight container at room temperature for 3 days or in the refrigerator for up to 5 days.
Freeze. Let muffins cool completely, then store in a freezer bag or container for up to 2 months. Thaw overnight in the fridge. 
Reheat. Warm in the microwave for 15-20 seconds.
Gluten-Free Flour Blends. Make sure your GF flour blend includes xanthan gum. If it doesn’t, add ½ teaspoon. Bob’s Red Mill 1:1 and King Arthur’s Measure for Measure both include it.”

Nutrition

Serving: 1muffin | Calories: 378kcal | Carbohydrates: 34.9g | Protein: 5.1g | Fat: 20.6g | Cholesterol: 61.5mg | Sodium: 221mg | Fiber: 2.6g | Sugar: 29.5g

Nutrition information is automatically calculated, so should only be used as an approximation.

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4.64 from 118 votes (114 ratings without comment)

14 Comments

  1. Bob says:

    1 star
    Really good!

    1. Molly T says:

      Thanks Bob!

  2. Molly Thompson says:

    I haven’t experience this at all!

  3. Becca says:

    5 stars
    Brought these to work and everyone loved them! They are so moist, very tasty, and the perfect size!

    1. Molly Thompson says:

      Thanks, Becca!!

  4. Eileen Cole says:

    5 stars
    Exceeded all expectations for gluten intolerant and tolerant family members! Delicious! Thanks!

    1. Molly Thompson says:

      What a compliment! Thank you so much!

  5. Tracey Brown says:

    5 stars
    These are amazing!!! Even my non gluten free husband and daughter think so! They didn’t believe me when I told them they were GF! Thank you!

    1. Molly Thompson says:

      Love that!! Thanks!

  6. Janice Minchin says:

    Can these be done WITHOUT EGGS, I have an egg allergy. I often use banana as a substitute. They look,and sound wonderful.

    1. Molly Leonard says:

      Hi Janice! Yes, you can definitely sub out eggs here. Use 1/4 cup of mashed banana to sub out one egg. Or you could to 1 tablespoon of ground flax seed with 3 tablespoons of water to sub out one egg! So for this recipe it would be 1/2 cup mashed banana or 2 tablespoons ground flax seed!

  7. Bethany says:

    Pumpkin chocolate chip muffins are the best! Yum!

  8. Jocelyn (Grandbaby Cakes) says:

    These muffins looks awesome!!

    1. Molly Leonard says:

      Thanks Jocelyn!