Featured Comment
From Lorna: “In the words of my toddler, in tears over these treats, “they’re just so good!” A really great recipe that brings the texture and moisture many gluten-free baked goods are lacking. Will be keeping this recipe close at hand”
From Sam: “These are my absolute favourite pumpkin muffins! Sooo good.”
From Abbie: “My family absolutely loves this recipe! I have been gluten free for over 6 years and this is one of the best pumpkin muffin recipes I have made. One that I am keeping on repeat this fall! Thanks for all your great recipes!”
Recipe Overview
⏱️ Time to Taste: 45 minutes
✨ Texture: Moist, fluffy, and light.
🥣 Ease: A simple recipe that’s easy to whip up whenever a pumpkin craving hits
🌾 Flour Used: Gluten-Free Measure-for-Measure Flour + Blanched Almond Flour
🧁 Equipment Needed: Standard muffin pan, mixing bowls, whisk, and rubber spatula
🎉 Best For: Fall breakfasts, snacks, lunchboxes, and holiday baking
❤️ Why You’ll Love It: These muffins are the kind of fall treat you’ll want to make on repeat. They’re soft, full of pumpkin flavor, and loved by both kids and adults.
As the weather gets cooler, there’s no better treat than a soft, spiced pumpkin muffin. This muffin recipe with pumpkin puree is packed with flavor and has the perfect tender texture. And they’re even better with mini chocolate chips added in!
If you’re looking for a delicious gluten-free muffin idea to satisfy your pumpkin cravings, this is a recipe you’ll come back to time and time again. Whether for breakfast, a snack or dessert, it’s one of my favorite gluten-free recipes for fall!
Ingredients You’ll Need
Here are a few notes on some of the key ingredients to make these gluten-free pumpkin muffins. Jump to the recipe card below for the exact measurements.
- Gluten-Free Flour: The type of flour you use can greatly effect how the muffins turn out. For best results, I recommend using King Arthur Gluten-Free Measure-for-Measure Flour.
- Almond Flour: I love adding a little almond flour because it adds moisture and richness for a tender texture. I recommend using blanched almond flour.. I also use a little in my gluten-free pumpkin chocolate chip bread!
- Spices: Cinnamon, nutmeg and cloves add warmth and enhance the pumpkin flavor for the coziest fall muffins! You can also use pumpkin pie spice instead.
- Pumpkin: Be sure to use 100% pure canned pumpkin, not pumpkin pie filling. It’s my go-to for all of my favorite gluten-free pumpkin recipes, like my classic gluten-free pumpkin bread!
- Oil: Any neutral oil works in this recipe! I like to use grapeseed, avocado, or vegetable oil. Coconut oil will work too.
- Lemon Juice: This might seem like an unusual ingredient, but adding a little lemon juice helps activate the baking soda and baking powder. This creates a little extra rise to ensure the fluffiest muffins!
How to Make the Best Gluten-Free Pumpkin Muffins
Here’s an overview of how to make these muffins. You can jump to the recipe for the full instructions!
Whisk dry ingredients: I like to mix the dry ingredients first so the leavening and spices are evenly distributed throughout the batter.
Whisk the wet ingredients: Mixing the wet ingredients separately helps create a uniform batter and even texture.
Combine: When adding the wet mixture to the dry ingredients be careful to not overmix! I stop mixing as soon as the flour is no longer visible. I love folding in some mini chocolate chips too!
Chill and Bake: I always chill the batter after scooping it into the muffin pan to give the gluten-free flours time to hydrate. I also recommend using the two-temperature baking method for tall, bakery-style muffins!
Make-Ahead/Storage/Freezing Instructions
To Make-Ahead: These muffins are best baked fresh, but you can make them ahead and store them once baked. They stay soft and moist when stored properly!
To Store: Store the cooled muffins in an airtight container at room temperature for up to 3 days or in the refrigerator for up to 1 week.
To Freeze: Let the muffins cool completely before transferring to a freezer bag or air-tight container. Freeze for up to 3 months. To thaw, let frozen muffins sit out at room temperature for a few hours.
What Do These Gluten-Free Pumpkin Muffins Taste Like?
These muffins taste like fall in every bite! They’re packed with fresh pumpkin flavor, warm spices, and just the right amount of sweetness. The cinnamon, nutmeg, and cloves create that classic pumpkin spice flavor without being overpowering.
Can I Use Pumpkin Pie Spice?
Yes! You can use 2 1/2 teaspoons pumpkin pie spice in place of the individual spices.
Can I Make Mini Muffins?
Yes! In fact, that’s one of my favorite ways to make this recipe! You can bake the gluten-free pumpkin muffins in a mini muffin pan, just reduce the bake time to 15-20 minutes. They’re perfect for parties and snacks!
More Gluten-Free Muffin Recipes
Moist Gluten-Free Pumpkin Muffins
Ingredients
Dry Ingredients
- 1½ cups (225g) gluten-free measure-for-measure flour
- ¼ cup (25g) almond flour
- 1 cup (200g) granulated sugar
- ½ cup (106g) brown sugar
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ¾ teaspoon kosher salt
- 2 teaspoons ground cinnamon
- ¼ teaspoon ground nutmeg
- ¼ teaspoon ground cloves
Other
- one 15-ounce can (425g) canned pumpkin puree
- 2 large eggs
- ⅓ cup (80ml) neutral oil
- 1 teaspoon vanilla extract
- 1 teaspoon lemon juice
- ½ cup (90g) mini chocolate chips, optional
Instructions
- Line a standard muffin pan with paper baking cups.
- In a large bowl, whisk together the gluten-free flour, almond flour, granulated sugar, brown sugar, baking powder, baking soda, salt, cinnamon, nutmeg and cloves.
- In a medium bowl, whisk together the pumpkin puree, eggs, oil, vanilla and lemon juice.
- Add the pumpkin mixture to the dry ingredients and stir with a rubber spatula until just combined and no dry flour streaks remain. Fold in the chocolate chips, if using.
- Using a kitchen scoop or large spoon, portion the batter evenly into the prepared muffin pan.
- Refrigerate the muffins for 20 minutes before baking. Preheat the oven to 425°F.
- Bake the muffins for 10 minutes at 425°F, then reduce the oven temperature to 375°F and continue to bake for 10-15 minutes, until a toothpick inserted into the center comes out clean.
- Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Notes
Nutrition
This post was originally published in September 2020. It was updated with new photos and instructions in July 2026.
These are amazing! I am trying to make for a kids’ class party and wondering if I could sub more gluten free flour blend in place of the almond flour? I want to make them totally allergen friendly!
Hi Kate, yes you can use more gf measure-for-measure flour in place of the almond flour to make them nut-free. We hope everyone enjoys the muffins!
Will this recipe work with flax or chia eggs? My granddaughter is allergic to eggs. Looking forward to trying this recipe
Hi Kay, with this recipe we would recommend trying Bob’s Red Mill egg replacer or something similar. We don’t recommend using flax eggs with these muffins. We hope this helps!
I made these today with coconut sugar and they came out great!
Can you please explain the purpose of refrigerating the muffins before baking? Thank you!!
We’re so glad you loved the muffins, Madeline! It’s great to know that sugar sub worked well too. Chilling the batter allows the gluten-free flour time to hydrate (prevents grittiness) and helps the muffins to bake up with taller domes for the best rise/shape. Great question!
These turned out so delicious! I used half the sugar and they were perfect! I used cupcake liners and for some reason they stuck really bad to the liner. (Might be an issue with the cupcake liners I bought?) Otherwise, an amazing recipe! Will make again! Also, I would love to know why the recipe has lemon juice? Thanks, Raya
Hi Raya, we’re so pleased you loved the muffins and that they worked well with that sugar reduction! Sometimes different brands of liners work better than others. We like these cupcake liners. Also, make sure the muffins cool completely before you try peeling the liners off. The lemon juice is the acid that activates the baking soda. It also can help with keeping the crumb tender and balancing the flavors. Happy baking!
My whole family loved these. They are super moist and fluffy. I cut the sugar and brown sugar in half and may reduce it slightly more next time.
I subbed 1/2 tsp pumpkin pie spinner of the cloves and nutmeg since I didn’t have them.
I slightly oiled the muffin pan instead of using liners.
This is a keeper for the family cookbook!
Yay! We’re so pleased to hear the recipe was such a hit with the whole family, Krystal! It’s good to know those adjustments worked well for you. Thank you for sharing your positive experience with us!
THESE ARE AMAZING! I love every recipe I have made from your page, but this is my new fav!
Yay! We’re so happy to hear you loved these muffins so much. Thank you for your kind feedback, Aileen!
I made these with a couple modifications and gave to my building staff and several physical therapists. Both groups said the best ever! Substituted the granulated sugar with Swerve granulated and could have the brown sugar with Swerve brown sugar. I was out of Almond flour and subbed coconut flower. Made muffins in their own decorative muffin paper cups and cooked 15 mins. Yum!!
Hi Diana, thank you for sharing your positive experience with us! We’re pleased to hear you enjoyed the muffins and that those substitutions worked well for you. Happy baking!
These are the best pumpkin muffins I’ve made! My daughters, one celiac and 2 not, ALL love them! I made a batch during the day and when the kids and their neighborhood friends got off the bus, the whole batch was gone! Moist, easy to make, delicious
Aww, we’re so glad the muffins were such a hit! Thank you for such amazing feedback, Gina!
Made these tonight and everyone in the family loved them. My girls said they couldn’t even tell they were gluten free!
Hi Kristen, thank you for your positive feedback! We’re happy to hear the muffins were a hit with the whole family!
Made these tonight and they’re tasty, absolutely love your recipes! While they tasted great, they were kind of thick/sticky and they stuck to the liner. I’m thinking I may have ended up over mixing them, but wanted to see what you think could have caused it.
Hi Lizzy, we’re so glad you enjoyed the flavor! Yes, overmixing can cause this issue. Other causes could be: too much moisture in the particular brand of pumpkin, underbaking or oven running cool, using a different gf flour blend, or trying to peel them from the liners while they’re still too warm. We hope these ideas help!
Super Soft and lasted for days on the counter in a container.
Thank you for your positive feedback, Ashley! We’re so pleased you enjoyed the muffin recipe!
Could you use regular flour ? And if so would you skip the almond flour ?
Hi Laurie, yes regular all-purpose flour should work as a 1:1 swap for the gluten-free flour. You can use it in place of the almond flour too. We hope you enjoy the muffins!
These are the most delicious muffins! They are moist and flavorful.I froze a couple and had an after-school treat for my grandsons. They loved them too. Erin has made be Gluten free pleasurable with her recipes .
Aww, we’re so pleased to hear the muffins were a hit with you and your grandsons! Thank you for sharing your positive experience with us, Lori!
Could this be baked in a loaf pan?
Thank you!
Hi Peggy, for a loaf version, we’d recommend this gluten-free pumpkin bread recipe. Happy baking!
These turned out great. I made half with chocolate chips sprinkled on top and half without. Both are delicious!
We’re so pleased you enjoyed the pumpkin muffins, Cindy! Thank you for your kind feedback!
This was really good Thanks!
We’re so glad you enjoyed the muffins, Kathleen! Thank you for sharing your positive feedback with us!
Made these with only 2 changes — reduced the sugar to 1 cup brown sugar only, and sprinkled with turbinado sugar before baking. The most delicious, moist, AWESOME gf pumpkin muffins we’ve ever eaten. Thank you for this recipe!! It will be saved in my “favorites” binder.
Hi Kara, we’re so happy to hear that this recipe has become a favorite! It’s good to know those sugar adjustments worked well too. Thank you for your kind feedback!