Gluten-free pumpkin muffins have become one of those little joys I look forward to every fall. As soon as the weather turns crisp and the leaves start tumbling, I pull out my favorite mixing bowl, turn on some music, and start measuring out warm spices and pumpkin puree. There’s just something about the smell of cinnamon and nutmeg filling the kitchen that makes the season feel official.
This recipe came together years ago when I was trying to find a gluten-free muffin that didn’t taste “gluten-free.” I wanted something soft and tender, made in one bowl, with the kind of cozy flavor you’d expect from a bakery. These gluten-free pumpkin muffins hit all the right notes—they’re gently sweet, full of pumpkin goodness, and easy enough for a weekday morning.
Whether you’re baking a batch for lunchboxes, sharing with neighbors, or just treating yourself to something warm on a chilly day, I hope this recipe brings a little bit of autumn comfort into your home—just like it does in mine.
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Why You’ll Love These Gluten-free pumpkin muffins
These Gluten-free pumpkin muffins aren’t just another fall treat—they’re a little bite of home, made to be shared, savored, or tucked into a lunchbox with love. Here’s why they’ve become a go-to in my kitchen:
– Naturally gluten-free and dairy-free – You won’t miss a thing. The texture is soft and tender, just like a classic pumpkin muffin.
– One-bowl recipe – No fancy equipment needed. You’ll have them mixed and in the oven in under 15 minutes.
– Warm, cozy flavor – Cinnamon, nutmeg, and real pumpkin come together for that classic autumn spice.
– Perfect for batch baking – Make a double batch and freeze some for later—you’ll be glad you did.
– Kid-friendly and lunchbox-ready – These are a hit with little ones, especially with a few chocolate chips or chopped pecans stirred in.
If you’ve been looking for a gluten-free pumpkin muffin that feels just as homey and delicious as the kind grandma used to make—this is it.
For another easy, cozy bake that uses pantry staples, try this healthy banana bread—it’s moist, simple, and full of flavor.
Ingredients for Gluten-Free Pumpkin Muffins
Here’s everything I use to make these cozy, gluten-free pumpkin muffins. You probably have most of it in your pantry already:
1 cup pumpkin purée (just plain pumpkin, not pie filling)
2 large eggs
½ cup light brown sugar
¼ cup maple syrup or honey—either one works
⅓ cup neutral oil (like avocado or vegetable oil)
1 teaspoon vanilla extract
1 ½ teaspoons ground cinnamon
¼ teaspoon ground nutmeg
¼ teaspoon ground ginger
½ teaspoon baking soda
1 teaspoon baking powder
¼ teaspoon salt
1 ¼ cups gluten-free all-purpose flour (make sure yours has xanthan gum)
Optional add-ins:
A handful of chocolate chips
Chopped walnuts or pecans
Sprinkle of raw sugar on top for a sweet little crunch
Feel free to adjust the spices or stir in your favorite mix-ins. This recipe is wonderfully forgiving—and always delicious.
How to Make Gluten-Free Pumpkin Muffins
- Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or lightly grease it. I like to use parchment liners so nothing sticks.
- Add in the cinnamon, nutmeg, ginger, baking soda, baking powder, and salt. Stir again to make sure those cozy spices are evenly mixed in.
- Gently fold in the gluten-free flour. Stir just until the batter comes together—don’t overmix. It should be thick but scoopable.
- If you’re adding chocolate chips or nuts, fold them in now. Save a few to sprinkle on top if you’d like.
- In a large mixing bowl, whisk together the pumpkin purée, eggs, brown sugar, maple syrup (or honey), oil, and vanilla. Mix until it’s smooth and well combined.
- Bake for 20–24 minutes, or until the tops are puffed and a toothpick inserted in the center comes out clean. Let them cool in the pan for 5 minutes, then transfer to a wire rack.
- Scoop the batter into your prepared muffin tin, filling each cup about ¾ full. Sprinkle a little raw sugar on top if you want a slight crunch.
These muffins are best warm, but they’re just as lovely the next day with a cup of tea or tucked into a lunchbox.
How to Customize These Gluten-Free Pumpkin Muffins
One of the things I love most about these gluten-free pumpkin muffins is how easy they are to adjust. Whether you’re baking for allergies, picky eaters, or just using what’s in your pantry, here are a few simple ways to make the recipe your own:
- Egg-free:
You can swap the eggs for two flax eggs (2 tablespoons ground flaxseed mixed with 5 tablespoons water). Let the mixture sit for a few minutes before adding it to the batter. - Nut-free:
Just skip the walnuts or pecans. These muffins are still full of flavor on their own, or you can toss in some pumpkin seeds for a bit of crunch. - Lower sugar:
You can cut the brown sugar to ⅓ cup or skip the maple syrup if you’d like a less-sweet muffin. The pumpkin still adds natural moisture and flavor. - Dairy-free:
These muffins are already naturally dairy-free as long as your chocolate chips (if using) are too. Always check the label! - Add-ins:
Stir in mini chocolate chips, dried cranberries, or even a swirl of almond butter. You can also add a scoop of protein powder or ground oats to make them more filling.
These little muffins are wonderfully flexible—make them work for you and your family.
Flavor Variations for Gluten-Free Pumpkin Muffins
Once you’ve made these cozy gluten-free pumpkin muffins a time or two, you might find yourself wanting to play with the flavors a bit. Here are a few of our favorite ways to switch things up:
- Pumpkin Chocolate Chip
Stir in ½ cup of semi-sweet or mini chocolate chips. A little melty chocolate with that warm spice? Always a yes in our house. - Maple Pecan
Swap the brown sugar for pure maple syrup and fold in chopped pecans. The combo is so rich and autumnal. - Cranberry Orange
Add ½ teaspoon orange zest and ½ cup dried cranberries for a bright, tangy twist that feels perfect around the holidays. - Pumpkin Spice Latte
Stir in 1 teaspoon instant espresso powder for a subtle coffee flavor that pairs beautifully with the cinnamon and nutmeg. - Mini Muffins for Little Hands
Use a mini muffin tin and reduce the bake time to about 12–14 minutes. These are great for kids or as a sweet little bite for brunch.
Each version still starts with the same easy base—just a few tweaks and you’ve got something new to share (or snack on while the rest are cooling!).
Love baking with pumpkin? These healthy pumpkin pancakes are another fall favorite in our home.
Storage & Freezing Tips for Gluten-Free Pumpkin Muffins
I always try to save a few of these gluten-free pumpkin muffins for later—but they tend to disappear fast! If you do manage to tuck some away, here’s how to keep them fresh and just as delicious as the day they were baked:
- Room Temperature:
Store muffins in an airtight container at room temperature for up to 2 days. I like to line the container with a paper towel to absorb any extra moisture. - Refrigerator:
If you need them to last a little longer, pop them in the fridge. Just warm them slightly before serving so they’re soft and cozy again. - Freezing:
These muffins freeze beautifully. Let them cool completely, then place them in a freezer-safe bag or container. You can freeze them for up to 2 months. - To Reheat:
Microwave a frozen muffin for 20–30 seconds or warm it in the oven at 300°F for about 10 minutes. It’ll taste like it just came out of the oven.
Sometimes I even freeze a few individually for quick weekday breakfasts—grab, zap, and go.
Frequently Asked Questions About Gluten-Free Pumpkin Muffins
Does Trader Joe’s have gluten-free pumpkin bread mix?
Yes, Trader Joe’s often carries a seasonal gluten-free pumpkin bread and muffin baking mix in the fall. It’s a popular option for quick baking, but I find that homemade recipes like these muffins have a softer crumb and richer pumpkin flavor—plus, you can control the sweetness and spices.
Is Libby’s pumpkin pie filling gluten-free?
Libby’s pure pumpkin purée is naturally gluten-free. However, their pumpkin pie filling (which includes added sugar and spices) may not always be certified gluten-free. It’s always best to read the label carefully. For this recipe, I recommend sticking with plain pumpkin purée for best results.
What is the secret to making moist muffins?
Moisture comes from a few things: real pumpkin, a good balance of oil, and not overbaking. I also love using a touch of maple syrup or honey—it keeps the crumb tender. Be careful not to overmix your batter, and always test with a toothpick near the end of the bake time.
Why are my gluten-free muffins dense?
Gluten-free flours can be a bit tricky. If your muffins are dense, it might be due to overmixing the batter, using a flour blend without xanthan gum, or adding too much flour. Make sure you spoon and level your flour—not scoop—and use a trusted 1:1 gluten-free blend. A little baking powder and soda helps give the lift you want.
Final Thoughts from Emma’s Kitchen
Gluten-free pumpkin muffins are one of those simple little joys that never get old—especially when the weather turns cool and the days call for something cozy. These muffins have become a fall tradition in our home, not just because they’re easy to make, but because they’re full of warmth, comfort, and the kind of flavor that brings people together.
If you’re new to gluten-free baking or curious about flour blends, this guide from King Arthur Baking is a wonderful place to learn more. It’s full of helpful tips on how to choose the right flour for different recipes.
Whether you’re baking a batch for your family, sharing them with a friend, or saving a few for quiet mornings with tea, I hope this recipe finds a happy place in your kitchen too.
And if you’re craving something savory to round out your fall table, this gluten-free chicken and dumplings makes a comforting main dish alongside your muffins.
If you give them a try, I’d love to hear how you made them your own—did you stir in chocolate chips, go nut-free, or try a mini version? Leave a note in the comments and let me know what you think.
