Gluten-Free Pumpkin Muffins

Healthy Gluten-Free Pumpkin Muffins you will fall in love with! These healthy pumpkin muffins are made with gluten free flour, coconut sugar, pumpkin and comforting pumpkin pie spices! 

Enjoy these gluten-free pumpkin muffins with a spread of homemade pumpkin butter. And use leftover pumpkin for gluten-free pumpkin chocolate chip cookies, or chocolate chip pumpkin muffins!

Jump to:
  • Why these gluten-free pumpkin muffins are so great
  • Flavor and Texture
  • Key Ingredients
  • How to make gluten free pumpkin muffins
  • Storing muffins
  • Recipe Tips
  • Benefits
  • More healthy pumpkin recipes
  • Gluten-Free Pumpkin Muffins

Why these gluten-free pumpkin muffins are so great

+ These are tender and moist gluten free pumpkin muffins and loaded with healthy ingredients! They are packed with tons of vegetables, fiber, and are gluten free with a grain free option using  Cassava Flour. These muffins are absolutely amazing and moist with warming pumpkin flavors bursting in every bite!

+ This healthy muffin recipe uses Diabetic-friendly coconut sugar, or you can use monk fruit or Xylitol to make sugar-free pumpkin muffins. They have the perfect amount of tender texture and sweet flavor. The natural sugars we use do not cause energy spikes and plummets. Plus, with the addition of pumpkin (or use any type of Cucurbita pepo, squash like canned butternut squash), your body and eyes will be praising you for the vibrant extra dose of vitamin A and fiber!

+Pumpkin muffins make a great snack year-round! Muffins are great to serve year-round as a healthy snack, breakfast, side dish, and anytime you are just home hanging out with the kids. This is a great recipe to make with them because they are totally kid-friendly and kids love to make muffins and cookies.

Flavor and Texture

  • delicious and sweet
  • moist and tender
  • robust and flavorful
  • quick veggie fix without tasting like vegetables
  • super soft and fluffy

Be sure to also check out more healthy muffins: healthy carrot muffins, banana zucchini muffins, banana nut muffins, apple carrot zucchini muffins.

Here’s what you’ll need to make these gluten free pumpkin muffins.

Key Ingredients

  • 1 (15 ounce) can pumpkin puree not pumpkin pie
  • eggs
  • ½ cup unsweetened apple sauce (or you can substitute it for ⅓ cup oil such as coconut oil or avocado oil)
  • coconut sugar or Xylitol or Monk fruit sugar
  • vanilla extract
  • gluten free flour – Pamela’s, Bob’s Red Mill 1-1 (the blue bag, not the red one), or Cup-4-Cup gluten-free flour. Use a dairy-free flour (not Cup-4-Cup) to ensure you are getting gluten-free dairy-free pumpkin muffins if dairy is an issue.
  • baking powder
  • baking soda
  • cinnamon
  • pink Himalayan salt
  • pecans chopped, optional for topping

How to make gluten free pumpkin muffins

STEP 1: Preheat the oven to 350 degrees F. Spray a silicone muffin pan or line a muffin pan with liners then spray them.

STEP 2: In a blender or medium bowl add the pumpkin, eggs, apple sauce and vanilla. Blend (of if using a bowl, whisk) to combine. In a large bowl mix together the flour, sugar, baking powder, baking soda, cinnamon and salt. Make a well in the center and add the wet ingredients to the dry ingredients and mix well to combine. You can also fold in chocolate chips at this point if you want to turn them into chocolate chip pumpkin muffins.

STEP 3: Divide the batter equally into the muffin pan. Add nuts to the top if you’d like (optional). Bake for 24-28 minutes or until slightly starting to brown on top and set in the center when a toothpick comes out clean.

Storing muffins

Store gluten-free pumpkin muffins in an airtight container and consume within 2-3 days. They do not need to be refrigerated, but if you do just warm them slightly to soften. To freeze the muffins place them in a freezer zip-lock bag and remove as much air as possible. Store in the freezer for up to 3 months. 

Recipe Tips

  • Measure the flour by scooping it with a spoon into a measuring cup then leveling it off with the back of a knife. Do not measure by scooping the measuring cup directly into the flour. Flour compacts during shipping and this can lend a dense muffin.
  • Use cupcake liners in a muffin pan and spray them with cooking oil for easy removal of the gluten-free pumpkin muffins after baking.


  1. Pumpkin: Pumpkin (a winter squash) gets its beautiful orange color from carotenoid pigments, including beta-cryptoxanthin, alpha and beta carotene which all provide vitamin A to the body and vitamin A enhances bone growth and improves eye sight. Pumpkins also have vitamin C  in them which Vitamin A and Vitamin C helps to boost the immunity. Good thing is they are available in cans year-round to make pumpkin pancakes, gluten-free pumpkin bread, chocolate chip pumpkin cookies, and muffins!
  2. Gluten Free Flours: For anyone with a gluten sensitivity or Celiac Disease you probably understand that consuming a gluten-free diet has made your body feel a whole lot better! Gluten is a binding agent that gives wheat products their elasticity. The results of long term eating gluten free are decreased stomach bloating, better bowl movements (helps cure diarrhea or constipation), decrease migraines, decrease ADHD and decrease symptoms of autism in children. You will get you all the details on that in my Dairy-Free Gluten-Free Baking Cookbook. There are lots of gluten free flour mixes like Bob’s Red Mill, Cup4Cup and Trader Joe’s and I really like using Cassava Flour for a grain free version. Cassava flour is made from Yuka root which is also a vegetable! It is highly dense so using lots of eggs keeps bread goods light and fluffy or in this case, pumpkin helps bind the flours together.
  3. Find great muffin baking tips also here.

More healthy pumpkin recipes

  • Gluten-Free Pumpkin Chocolate Chip Muffins
  • Pumpkin Soup
  • Pumpkin Breakfast Cookies
  • Pumpkin Pancakes
  • Gluten-Free Pumpkin Bread
  • Gingerbread Pumpkin Trifle
  • Pumpkin Hummus
  • Pumpkin Cookies
  • Gluten-Free Pumpkin Chocolate Chip Cookies
  • Homemade Pumpkin Butter
  • Grain-Free Pumpkin Muffins

I hope you enjoy this gluten-free pumpkin muffins recipe! Follow along with me on INSTAGRAM, PINTEREST, FACEBOOK, YOUTUBE and TWITTER for a feature and for more recipe inspiration! And don’t forget to give the recipe a star rating in the recipe area and leave a comment below.

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