Healthy, Gluten-Free Pumpkin Muffins

Healthy, gluten-free pumpkin muffins are a soft, tender muffin made with healthier swaps, like less oil and less sugar for a light, healthy muffin perfect for fall!

a pile of pumpkin muffins with one broken in half, facing up

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And just like that, the last pumpkin muffin recipe from NTF’s pumpkin palooza is here! We started with pumpkin chia pudding, then headed savory with pumpkin pasta sauce. Today? I’m sharing a healthy pumpkin muffin recipe that has been tested many times and is loved by my family!

What makes these healthy pumpkin muffins?

Healthy is subjective – and that’s okay. Find nutrition to fit your life! But for these gluten-free muffins I focused on some healthier ingredient swaps:

  • Decreased the amount of sugar.
  • Decreased the amount of oil.
  • Added applesauce for additional subtle sweetness (in place of more sugar) and more moisture (instead of more oil).
  • A full cup of pumpkin for festive fall flavor, moisture and tenderness, and all the pumpkin nutrition benefits.

Additionally, pumpkin itself is an incredibly nutrient-dense food that offers nutrients like fiber, vitamins A, E, K, C, folate, and iron. These nutrients can help promote health benefits associated with pumpkin, like improved immunity, heart health, eye health, skin health, and may lessen risks of certain cancers (see linked article for references).

pumpkin muffins in a metal pan with cinnamon sprinkled on top

How to Make Gluten-Free Pumpkin Muffins

To make these gluten-free pumpkin muffins, you need the following ingredients:

  • Pumpkin puree
  • Eggs
  • Avocado oil
  • Vanilla extract
  • Brown sugar
  • Applesauce (unsweetened)
  • Gluten-free measure-for-measure flour
  • Baking powder
  • Baking soda
  • Pumpkin pie spice
  • Optional add-ins, like chocolate chips, raisins, chopped nuts, pumpkin seeds, dried cranberries, etc.

From there, it’s pretty straightforward! Whisk together all the wet ingredients in a large bowl, then stir in the dry ingredients.

Since these muffins are a little lower in fat than many others, I find they can sometimes stick to a parchment muffin liner a little bit, so I actually personally prefer to use a little non-stick spray (olive or avocado) in the muffin tins.

Scoop the batter into the muffin tins. You can leave as is or sprinkle the tops with a little cinnamon (like I did) or garnish with mix-ins you may have used.

Bake for 18-20 minutes, or until an inserted toothpick comes out clean. Let cool in the muffin tin a few minutes, then enjoy!

Holding half a pumpkin muffin to show the light, fluffy texture of this easy, gluten free muffin.

Ingredient Substitutions

I have not tested it this way, as I have to eat gluten-free, but I’ve heard from testers that whole wheat flour and whole wheat pastry flour work in this recipe if you tolerate wheat.

For gluten-free flours, I used King Arthur Gluten-Free Measure for Measure Flour – my favorite! I’ve tried making with oat flour, and while they were acceptable, I found the oat flour muffins to be a little more dense and not quite as fluffy (but it is a whole grain option!).

As far as other substitutions, check out the following:

  • If you’re egg-free (or out of eggs) try a flax egg. Mix 1 tbsp ground flax seed with 3 tbsp warm water, stir, and let sit a few minutes. The flax will gelatinize and your flax egg is ready when it is thicker, kind of like egg whites!
  • You can use most any other preferred oil instead of avocado oil, even olive oil. While you can use coconut oil or butter, I found through recipe testing that they make the finished pumpkin muffin slightly denser.
  • Cinnamon can be used instead of pumpkin pie spice. It has a slightly less diverse flavor profile, but still tastes great!
  • And I know this sounds silly, but if you really want these muffins and are out of pumpkin, try using pureed butternut squash or sweet potato!

A note on sugar:

I’ve had a few questions asking why I used brown sugar in this healthy pumpkin muffin recipe as opposed to something like coconut sugar, maple syrup, or honey.

Honestly? It’s three-fold:

  1. At the end of the day, sugar (even more “natural” sources like maple syrup) is used by our body as sugar. I prefer to focus on a lower amount of sugar of any kind as opposed to a higher amount of natural sugars. As a dietitian, I feel overall that the amount of added sugar used has a bigger impact on health than the type of added sugar.
  2. There are already a lot of ingredients that provide moisture to these muffins – pumpkin, applesauce, oil, eggs, etc. While each ingredient serves a different purpose, I was concerned the texture was off when using a liquid sweetener like honey or maple syrup.
  3. Brown sugar is cheaper. I want my recipes to be accessible to more people. Plus, y’all, I’m on a budget, and when I test baking recipes usually at least 4-5 times, it’s a lot more economical to use brown sugar than maple syrup or honey!

Versatile Add-Ins

These easy pumpkin muffins are delicious enough on their own, but also make an incredibly versatile gluten-free pumpkin muffin. Try some of our favorite additions! My husband and I love adding pumpkin seeds and dried cranberries, whereas my toddler sous chef always requests the addition of chocolate chips. 😉 Get creative! We find a half cup of any addition to be the perfect amount.

pumpkin muffins in a silver pan - the top row with chocolate chips, the middle row with cinnamon, and the bottom row with raisins and pumpkin seeds.

Use in Meal Prep

These easy pumpkin muffins are quite versatile. They can be made for breakfast, snacks, and we’ve even enjoyed them as a dessert. They’re fluffy and delicious enough that I’m planning on making them on Thanksgiving, but also simple enough that we make them as part of a grab-and-go breakfast.

Grab one of these pumpkin muffins and pair it with a couple hard-boiled eggs or some greek yogurt for some protein, and maybe grab a piece of fruit, too. You can also top it with some sunflower seed butter for some more healthy fats!

More Pumpkin Recipes

For more pumpkin fun, check out these additional pumpkin recipes:

If you like this recipe be sure to comment and rate it below and share on PinterestInstagram, and Facebook. Live well!

a pile of pumpkin muffins with one broken in half, facing up

Healthy, Gluten-Free Pumpkin Muffins

Healthy, gluten-free pumpkin muffins are a soft, tender muffin made with healthier swaps, like less oil and less sugar for a light, healthy muffin perfect for fall!
free from: wheat/ gluten, soy, dairy, fish, shellfish, peanuts, tree nuts
4.72 from 7 votes
Print Pin Rate
Course: Breakfast, Snack
Cuisine: American
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 12
Calories: 129kcal
Author: Lindsey Janeiro, RDN, LDN


Wet Ingredients

  • 1 cup pumpkin puree
  • ¼ cup avocado oil (or other neutral oil)
  • ¼ cup unsweetened applesauce
  • ¼ cup brown sugar
  • 2 eggs
  • 1 tsp vanilla extract

Dry Ingredients

  • 1.5 cups gluten-free measure-for-measure flour (I used King Arthur brand)
  • 1 tsp pumpkin pie spice
  • 1 tsp baking powder
  • ½ tsp baking soda
  • ¼ tsp salt

Optional Mix-In Ingredients:

  • ½ cup chocolate chips
  • ½ cup dried fruit (like raisins or dried cranberries)
  • ½ cup seeds or chopped nuts
  • ½ cup any combination of the above
  • cinnamon to sprinkle on top


  • Preheat oven to 350F. Prepare a muffin tin by lightly coating each tin with non-stick spray.
  • Whisk together wet ingredients in a large bowl. Stir in dry ingredients and any optional mix-in ingredients.
  • Scoop batter into prepared muffin tins. Sprinkle tops with cinnamon, or top with a tablespoon of any toppings (i.e. chocolate chips or pumpkin seeds).
  • Bake for 18-20 minutes, or until an inserted toothpick comes out clean. Let cool for a few minutes, or until muffins are cool enough to handle, and transfer to a wire baking sheet.


Muffins keep at room temperature up to 3 days, in the fridge up to 5-6 days, and in the freezer up to 3 months. To thaw, thaw overnight on the counter or in the microwave for 30 seconds.


Calories: 129kcal | Carbohydrates: 18g | Protein: 3g | Fat: 6g | Saturated Fat: 1g | Cholesterol: 27mg | Sodium: 114mg | Potassium: 104mg | Fiber: 2g | Sugar: 6g | Vitamin A: 3217IU | Vitamin C: 1mg | Calcium: 42mg | Iron: 1mg

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Healthier, Gluten-Free Pumpkin Muffins

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  1. When you initially made the gluten free pumpkin (with applesauce) muffins recipe before you put it on your blog online did it taste bland like it did when I made it? I used 2 cups gluten free, non GMO oat flour, 1/4 cup coconut oil, then while pouring unsweetened applesauce out of a can too much came out, so I added some more oat flour, had to add 4 packets of Stevia, maybe the outdated pumpkin pie spice s why it turned out blah? I followed the recipe best I could. I didn’t fancy using organic brown sugar when it causes me to feel uncomfortable. I baked the muffins for 10 or 15 minutes, then checked the inside and saw they were quite moist so I added some brown sugar with a spoon after I opened the top of the muffins and placed them back in the oven and baked ’em 10 more minutes. Big mistake! The extra amount of brown sugar just made it taste overly sweetened, but I were trying to make it taste better. I had to bin ’em when I expected to have some for breakfast. It’s nowt to do with you, but sure made me feel like a daft bint.

  2. The only thing I had to do to add extra flavor to the recipe was to double the pumpkin pie spice and that made all the difference! So for anyone saying it’s too bland, dont shy away from a bit of extra spice, it smells pungent but once it’s cooked it’s really good! Dont stray too far from the recipe either or it will not come out well. I used king Arthur’s measure for measure flour, and I used an egg replacer, they are nice and soft and taste really good.

  3. Love the taste but they were too wet and dense, even cooked them for 25 min to see if it would dry them out but it didn’t. I did use coconut oil and I only had Bob’s Red Mill 1:1 GF flour so I used that. Otherwise all the same ingredients and amounts. What do I need to adjust to have them be a “normal” texture?
    I have to eat GF also so I would really like to figure this out as I love pumpkin!
    Thanks! Tracy

    1. Hi Tracy! It’s always so hard to troubleshoot without being there/ seeing the process! I’ve made these with Bob’s Red Mill 1:1 GF flour before, so that should’ve been fine. I haven’t used coconut oil in this recipe, but so long as you stuck to the 1/4 cup oil measurement, I have a hard time believing the coconut oil would make that big of a difference. And you only used 1 cup of pumpkin puree and not 1 can? And it was pumpkin puree and not the canned pumpkin pie filling? Where do you live – could there be any altitude factors at play? I’d like to help you figure this out, too! Feel free to send me an email at [email protected] if that’s easier! Good luck!

  4. The texture of these is wonderful, but not much flavor at all. I make my own pumpkin pie spice (cinnamon, ginger, nutmeg & allspice) & doubled the amount, and added some chocolate chips… still not much flavor. I used coconut sugar instead of brown and definitely would recommend more sweetener next time.

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