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Home » Recipes » Breakfast Recipes

Healthy Pumpkin Muffins (Gluten Free) That Taste Like Fall

Modified: Jul 29, 2026 by Kori Butler

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Gluten free pumpkin muffins are everything I want in a cozy fall bake - soft, moist, warmly spiced, and surprisingly wholesome. Made with almond flour, pumpkin puree, and a sugar-free sweetener, they're a healthy breakfast or snack that tastes like pumpkin season in every bite.

Healthy Pumpkin Muffins (Gluten Free)Pin
Jump to:
  • The backstory.
  • It's a must-make.
  • Let's talk texture and flavor.
  • What you'll need.
  • Customize it your way.
  • Flexible dietary swaps.
  • How to make pumpkin muffins (gluten free).
  • How to enjoy them.
  • Kori's tips.
  • FAQ's
  • 📖 The recipe.
  • Keep the good eats going.
  • 💬 What readers are saying.

The backstory.

I love having recipes that make healthy eating feel a little more fun, especially during the fall. These gluten free pumpkin muffins have become one of my go-to breakfast bakes because they're easy to make ahead, full of cozy pumpkin spice flavor, and perfect for grabbing on busy mornings. They're the kind of recipe I find myself making more than once every pumpkin season.

xoxo Kori

It's a must-make.

If you're looking for gluten free pumpkin muffins that are easy, satisfying, and packed with cozy fall flavor, this recipe is about to become a seasonal favorite.

  • Soft, moist, and perfectly spiced. Every bite is tender with just the right balance of pumpkin, warm spices, and vanilla.
  • A healthier way to enjoy pumpkin season. Made with almond flour and a sugar-free sweetener, these muffins are naturally gluten-free, low carb, keto, sugar-free and a delicious option for breakfast or an afternoon snack. These can easily be made dairy-free by using coconut oil instead of butter!
  • Perfect for make-ahead mornings. Bake a batch once and enjoy fresh-tasting muffins throughout the week, or freeze extras for busy mornings.
  • Easy enough for any baker. No fancy techniques or complicated ingredients - just simple mixing, baking, and enjoying.

Nothing says Fall like pumpkin. Enjoy these tasty gf muffins with a hot cup of coffee on a chilly Fall morning and you'll be in your happy place.

Let's talk texture and flavor.

These GF pumpkin muffins are wonderfully soft with a moist, tender crumb thanks to the pumpkin puree and almond flour. Pumpkin pie spice brings all those classic fall flavors - cinnamon, nutmeg, ginger, and cloves - without overpowering the pumpkin itself. The vanilla rounds everything out while the lightly sweet batter lets the warm spices shine. They're delicious on their own, but they're even better with a little butter or pumpkin cream cheese frosting.

What you'll need.

Image of ingredients needed to make gluten-free pumpkin muffins.Pin

These gluten-free pumpkin muffins come together with simple pantry ingredients that work together to create a bakery-worthy muffin with wholesome ingredients and plenty of fall flavor.

  • Blanched almond flour: Finely ground almond flour creates a soft, tender crumb while keeping these gluten free muffins naturally low carb.
  • Allulose or monkfruit sweetener: A 1:1 sugar substitute provides sweetness without added sugar.
  • Pumpkin pie spice: The classic blend of warm spices that gives these muffins their signature fall flavor.
  • Gluten free baking powder: Helps the muffins rise into beautiful domed tops.
  • Salt: Balances the sweetness and enhances all of the flavors.
  • Xanthan gum: An important ingredient that improves texture and helps hold the muffins together. Don't skip it.
  • Pumpkin puree: Adds moisture, flavor, and that gorgeous golden-orange color.
  • Butter or coconut oil: Melted butter adds rich flavor, while coconut oil is a great dairy-free alternative.
  • Large eggs: Provide structure and help create a light, fluffy texture.
  • Vanilla extract: Adds warmth and enhances the pumpkin and spice flavors.

If you're like me, once pumpkin season starts, one recipe usually turns into three. Pair these Healthy Pumpkin Muffins with my Maple No Bake Pumpkin Protein Balls for an easy grab-and-go snack, bake a pan of Cozy Pumpkin Baked Oatmeal for a weekend breakfast everyone can enjoy, or prep Pumpkin Overnight Oats for those mornings when you need breakfast waiting in the fridge. With a few make-ahead favorites like these, enjoying cozy fall flavors all week long couldn't be easier.

Customize it your way.

Whether you're adding a little extra sweetness, a fun mix-in, or a different spice, it's simple to make these pumpkin muffins (gluten free) your own.

  • Stir in ⅓ cup sugar-free chocolate chips for a chocolatey pumpkin treat. Gluten free pumpkin chocolate chip muffins are delicious!
  • Swap the vanilla extract for maple extract for an extra cozy fall flavor.
  • Sprinkle chopped pecans or walnuts over the tops before baking for added crunch.
  • Add a few unsweetened coconut flakes to the batter for a subtle tropical twist.
  • Top the cooled muffins with the pumpkin cream cheese frosting from the recipe card when you're craving something a little more dessert-like.
  • Sprinkle a pinch of pumpkin pie spice over the batter before baking for an extra pretty finish.

Flexible dietary swaps.

Gluten free pumpkin muffins are easy to adapt to your needs while still keeping that delicious pumpkin flavor.

  • Dairy-Free: Use melted coconut oil instead of butter.
  • Sugar-Free: Stick with allulose or monk fruit sweetener with a 1:1 sugar ratio as written.
  • Paleo-Friendly: Use coconut oil and a paleo-approved granulated sweetener along with gluten-free baking powder that fits your needs.
  • Vegetarian: This recipe is naturally vegetarian.
  • Lower Sodium: Reduce the added salt slightly if you're watching sodium, but keep enough to balance the flavors.

How to make pumpkin muffins (gluten free).

Gluten free pumpkin muffins come together in just a few simple steps and bake up soft and tender every time.

  1. In one bowl, stir together the almond flour, sweetener, pumpkin pie spice, baking powder, salt, and xanthan gum until everything is evenly combined.
  2. In a separate bowl, whisk together the pumpkin puree, eggs, melted butter (or coconut oil), and vanilla until smooth.
  3. Fold the wet ingredients into the dry ingredients and stir just until no dry spots remain. Be careful not to overmix.
  4. Divide the batter evenly between the prepared muffin cups and bake until the tops are lightly golden and a toothpick inserted into the center comes out clean.
  5. Let the muffins cool for several minutes before transferring them to a wire rack.
Healthy gluten free pumpkin muffins set out on a cake stand.Pin

How to enjoy them.

These gluten free pumpkin muffins are delicious warm from the oven, but they're just as handy to have around for quick breakfasts and snacks throughout the week.

  • Enjoy one warm with a little butter for an easy breakfast.
  • Spread with pumpkin cream cheese frosting for a special fall dessert.
  • Pair with Greek yogurt and fresh berries for a balanced breakfast.
  • Serve alongside a hot cup of coffee, chai tea, or a pumpkin spice latte.
  • Pack one in lunchboxes or keep a few on hand for an afternoon snack.
  • Add them to a fall brunch spread with eggs, fresh fruit, and turkey sausage.

Kori's tips.

  • Don't skip the xanthan gum. It helps hold the muffins together and gives them a better texture.
  • Stir just until combined. Overmixing can make almond flour baked goods denser than they need to be.
  • Test with a toothpick. Insert it into the center of a muffin. If it comes out clean, they're ready. Let them cool for about 5 minutes before removing them from the pan. They'll be easier to lift out without breaking.
  • Want extra smooth batter? Whisk the wet ingredients thoroughly before combining with the dry ingredients.
  • Make a double batch. These freeze beautifully, making breakfast easy all season long.

FAQ's

What's the best way to store it?

Store completely cooled muffins in an airtight container at room temperature for up to 2 days or refrigerate them for up to 5 days.

Can I freeze them?

Yes, absolutely. You can freeze these gluten free pumpkin muffins. I will often make a large batch of these, then once cooled, I place them in an airtight container or plastic freezer bag. Freeze for up to 3 months. They never last that long, of course. 🙂

Why is xanthan gum important?

Because these muffins are made with almond flour and don't contain traditional wheat flour, xanthan gum helps improve the texture and keeps the muffins from crumbling. It's a small ingredient that makes a big difference.

Can I use granulated monk fruit sweetener instead of allulose?

Yes!  You can use any granulated sweetener as long as it has a 1:1 sugar ratio. I tested granulated monk fruit and allulose, and both came out great.

📌 Be sure to save this pin to Pinterest for later!

Gluten Free Fall-Inspired Gluten Free Pumpkin MuffinsPin

Can I ask you a favor?

If you tried this recipe, let me know! I'd love for you to come back and give the recipe a 5 star rating and leave a review in the comments! 🙂 Let's stay connected, so please follow me on YouTube, TikTok, Instagram, Facebook, and Pinterest! Subscribe to my newsletter to get healthy fresh recipe ideas every week!

📖 The recipe.

square feature image of two gluten free pumpkin muffins stacked on top of each other with a small pumpkin in the background.

Recipe For Gluten-Free Pumpkin Muffins

These Healthy Pumpkin Muffins (Gluten Free) are soft, moist, and packed with warm pumpkin spice flavor. Made with almond flour and pumpkin puree, they're perfect for breakfast, snacks, or meal prep. Gluten-free, low-carb, keto, sugar-free pumpkin muffins.
5 from 2 votes
Print Recipe Pin Recipe Save Saved!
Author Kori Butler
Prep Time 10 minutes mins
Cook Time 25 minutes mins
Total Time 35 minutes mins
Course Breakfast
Cuisine American
Servings 12 servings
Calories 145 kcal

Ingredients
  

  • 2½ cups finely ground blanched almond flour
  • 1 cup allulose or monkfruit sweetener (with a 1:1 sugar ratio)
  • 4 teaspoons pumpkin pie spice
  • 4 teaspoons gluten free baking powder
  • ½ teaspoon salt
  • ½ teaspoon xanthan gum
  • ⅔ cup pumpkin puree
  • ½ cup butter or coconut oil (melted but not hot)
  • 4 large eggs
  • 1 teaspoon vanilla extract

Instructions
 

  • Preheat oven to 350F. Stir together almond flour, sweetener, baking powder, pumpkin pie spice, salt, and xanthan gum in a medium bowl.
    Mixing dry ingredients in a clear glass bowl
  • In a second bowl, whisk together eggs, pumpkin puree, melted butter, and vanilla.
    Mixing wet ingredients in a clear glass bowl
  • Add the wet ingredients into the dry and stir until just combined.
  • Line a 12-cup muffin tin with paper liners. Spoon approximately ¼ cup of batter into each cup.
  • Bake for 25 to 28 minutes or until a toothpick inserted in the center comes out clean.
  • Cool the donuts for 5 minutes, then carefully loosen and remove from the pan. Let muffins cool on a rack. Once cooled, store in an airtight container or plastic bag.

Video

Kori's Tips

  • Don't miss all of our helpful hints, substitution ideas, cooking tips, and other delicious recipes that can be found in our post. Check it out!
  • PUMPKIN CREAM CHEESE FROSTING: In a small bowl, mix 2 ounces of very soft cream cheese, 4 tablespoons powdered sweetener, ¼ teaspoon vanilla, 1 tablespoon pumpkin puree, and 2 tablespoons heavy cream. 
  • MAKE PUMPKIN CHOCOLATE CHIP MUFFINS: Add a ⅓ cup sugar-free milk chocolate or white chocolate chips. You will need to increase the recipe time slightly. 
  • TIPS: Do not substitute or leave out xanthan gum; Test the muffins for doneness by using a toothpick and inserting in the center. If the toothpick comes out clean, the muffins are done. 

Nutrition

Serving: 1muffingCalories: 145kcalCarbohydrates: 7.5gProtein: 5.7gFat: 13.5gSaturated Fat: 5.4gCholesterol: 82.3mgSodium: 129.2mgFiber: 1.5gSugar: 1.4g
DID YOU MAKE THIS RECIPE?Mention @seekinggoodeatsofficial or tag #seekinggoodeats! Be sure to subscribe to my newsletter to receive more healthy delicious recipes straight to your inbox.

© 2025 Seeking Good Eats™

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Reader Interactions

Comments

  1. Manya Phillips

    March 02, 2023 at 11:20 am

    Made these yesterday. I ended up with 21 muffins. So my carb count went down to 3 I think.Oh my they are so so so tasty. I will be making these over and over again. Thank you💕💕

    Reply
    • seekinggoodeats

      March 12, 2023 at 9:33 am

      Oh good! Thank you for trying the recipe out. I'm so glad you ended up with more - and you loved them. 🙂 I love how moist they turn out

      Reply
5 from 2 votes (2 ratings without comment)

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Hey there, I'm Kori.

I’m a culinary school trained chef specializing in holistic nutrition and wellness. I’ve always been a major foodie, and as I’ve aged, the full impact of my love of food—and not-necessarily-healthy eating habits—caught up to me. In an effort to make positive changes in my life (and hopefully yours, too), I created this website where I could share great-tasting, craveable, healthy recipes.

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