These Healthy Pumpkin Muffins are gluten-free, quick and easy-to-make, and are topped with the BEST streusel crumble. This fluffy fall recipe is full of pumpkin pie spices and is healthy enough to eat for a cozy Thanksgiving breakfast or afternoon snack! 

Want a few other healthy muffin recipes?  You might also enjoy these Lemon Poppy Seed MuffinsHealthy Banana Nut MuffinsHealthy Lemon Zucchini Muffins, and these Paleo Chocolate Banana Muffins.

Three gluten-free pumpkin muffins stacked on top of each other surround by other healthy, vegan, and easy pumpkin muffins.

Healthy Pumpkin Muffins Season

It’s pumpkin season!!!

Pretty much as soon as the calendar strikes September, it is full-on pumpkin season in our house.  (And maybe a little bit of Apple Crisp season, too!)

From Pumpkin Chocolate Chip Cookies, to the BEST Vegan Pumpkin Pie, our house is constantly smelling like a delightful Bath & Body Works candle.

(OK, maybe there is one of those burning in my office non-stop, too!)

A pumpkin muffin with a bite taken out of it next to two other pumpkin streusel muffins.

A Healthy Snack for Relay Runners

Just a few weeks ago we had a relay race here in Austin.

Knowing a bunch of our running group friends would be pretty hungry after the race, I decided to bring them a batch of fluffy, healthy, and gluten-free pumpkin muffins.

I will be honest, though… it took me a couple of batches to get the spice level just right and to get that perfectly fluffy and not-too-moist texture.

And friends… this recipe is seriously the BEST fall inspired recipe you have ever tasted.  (Voted on by 20+ VERY hungry runners!)

Not to mention, it has a crispy and crumbly streusel topping that is out-of-this-world delicious.

Gluten-free pumpkin muffin recipe ingredients laid out on a black background.


The ingredients needed for this pumpkin muffin recipe are relatively simple and easy-to-find.  There are also quite a few substitutions you can try to make these gluten-free and vegan.

  • Pumpkin – This is the main ingredient and gives the bulk of the flavor to these muffins.  Read more below about the benefits of using canned puree versus homemade.
  • Flour – A gluten-free 1-to-1 flour blend is used in this recipe.  If you are not gluten-free, you can always use regular all-purpose flour instead.  You can also make your own homemade gluten-free flour.
  • Coconut Oil – You can also use butter if you are not vegetarian or vegan, or a vegan butter substitute if you are dairy-free or vegan.
  • Egg – Only one egg is needed to help hold these muffins together.  If you’re vegan or allergic to eggs, you can use a flax egg instead.
  • Coconut Sugar – A natural, refined sugar-free sugar is used in place of regular sugar.  However, if you do not have coconut sugar, you can also use regular, white granulated sugar instead.
  • Pumpkin Pie SpiceStore bought pumpkin pie spice is the easiest spice to use, but if you don’t have one you can always make your own homemade pumpkin pie spice.

A big bite that has been taken out of a gluten-free pumpkin streusel muffin.

Canned Puree or From Scratch?

It is completely up to you!  Using a store bought canned pumpkin puree is definitely the easiest and fastest way to make these muffins.

But, if you’ve got a taste for the finer things in life, making homemade pumpkin puree always gives baked goods a little extra bit of love.

If buying canned puree, make sure you look for a good organic brnad for the best taste, texture, and nutrition.

Streusel topping that is being mixed together in a clear bowl for a healthy pumpkin muffin recipe.

Streusel Topping

A streusel topping typically consists of some type of flour, fat, and sugar.

In order to make this streusel topping both gluten-free and refined sugar-free we will be using a gluten-free flour blend and coconut sugar.

If you would like to take it a step further, you can also use coconut oil or a vegan butter substitute in place of the butter to make a vegan streusel topping.

How to Make a Streusel Topping:

  1. Add the butter, sugar, flour, and cinnamon to a medium-sized bowl.
  2. Cut ingredients with a fork or pastry cutter until the streusel topping resembles coarse crumbs and sticks together when pushed between two fingers.

Cook’s Tip: To ensure the crumble is the right consistency, make sure the butter is softened and almost melted before mixing.

Streusel muffins with white cupcake liners in a muffin tray.

The Best Gluten-Free Flour to Use

As mentioned previously, a gluten-free flour blend is used in this recipe to make these pumpkin muffins safe for Celiacs.

In the past, I made my own homemade gluten-free flour blend.  It worked out great in most recipes, but took a little extra time to prepare.

Recently, Bob’s Red Mill came out with the best gluten-free 1-to-1 flour blend that replaces regular all-purpose flour cup-for-cup in just about any recipe.

There are other gluten-free flours out there, but they were not tested with this recipe.

Four images showing how to make pumpkin muffins with healthy, gluten-free, and vegan ingredients.

How to Make

This healthy pumpkin muffin recipe consists of the same steps and processes as other muffin or quick bread recipes do:

  1. Preheat oven to 350°F.
  2. Mix together dry ingredients in a large bowl. (Image 1 above.)
  3. Whisk together wet ingredients in a separate bowl. (Image 2 above.)
  4. Combine wet and dry ingredients and mix until combined. (Images 3 and 4 above.)
  5. Cut streusel topping together.
  6. Place liners into 12 muffin cup cavities and spray with non-stick cooking spray.
  7. Fill liners with batter until they are almost full. (Image 1 below.)
  8. Sprinkle streusel topping on top of batter. (Image 2 below.)
  9. Bake in preheated oven for 24-26 minutes, or until toothpick when inserted in comes out clean.Pumpkin muffin batter in a muffin cup tray before and after being baked in the oven.

Serving, Storing, and Freezing

How to serve?

Let muffins cool to room temperature and serve immediately.  You can also cut them in half, butter the halves, and then toast in a toaster oven until edges are crispy.

How long will they last?

Pumpkin muffins will last in an airtight container at room temperature for 2-3 days or in the refrigerator for up to 4-5 days.

Can I freeze pumpkin muffins?

Yes, you can freeze this recipe. Place muffins in an airtight Ziploc bag or container and freeze for up to 4-6 months.

A tray full of an easy pumpkin muffin recipe next to a bottle of pumpkin pie spice and pumpkin puree.

Other Healthy Pumpkin Recipes

Healthy Pumpkin Chocolate Chip Cookies

The Best Grain-Free Vegan Pumpkin Pie

Pumpkin Pancakes | Paleo

Coconut Flour Pumpkin Bread with Crumb Topping

Pumpkin Oatmeal Muffins

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4.41 from 5 votes

Healthy Pumpkin Muffins | Gluten-Free

These Healthy Pumpkin Muffins are gluten-free, quick and easy-to-make, and are topped with the BEST streusel crumble. This fluffy pumpkin muffin recipe is full of pumpkin pie spices and is healthy enough to eat for a cozy Fall or Thanksgiving breakfast or snack!
A big bite that has been taken out of a gluten-free pumpkin streusel muffin.
Yield 12 muffins
Prep 10 minutes
Cook 25 minutes
Total 35 minutes
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  • 2 cups flour gluten-free, 1-to-1
  • ¾ cup coconut sugar
  • 1 tsp. baking soda
  • 1 ½ tsp. pumpkin pie spice
  • ½ tsp. salt
  • ¾ cup pumpkin puree homemade or canned
  • 1 egg whisked
  • cup coconut oil melted
  • cup pure maple syrup room temperature
  • ½ cup milk cashew or almond milk
  • 1 1½ tsp. vanilla extract

Streusel Topping:

  • cup flour gluten-free, 1-to-1
  • 2 Tbsp. butter softened, almost melted
  • 2 Tbsp. coconut sugar
  • ½ tsp. cinnamon


  • Preheat oven to 350 degrees.
  • In a large bowl combine flour, coconut sugar, baking soda, pumpkin pie spice, and salt. Whisk until combined.
  • In a separate bowl combine the pumpkin puree, whisked egg, melted coconut oil, maple syrup, milk, and vanilla extract. Whisk until well combined.
  • Slowly add dry ingredients to wet ingredients, mixing well after each addition, until all ingredients are combined.
  • For the streusel topping: Combine the ingredients in a medium-sized bowl. Using a fork or pastry cutter cut the ingredients together until the mixture forms coarse crumbs.
  • Line a 12-count muffin tray with cupcake liners and spray with non-stick cooking spray. Fill each cavity with ~⅓ cup batter, or until almost full. Sprinkle equal amounts of streusel topping on each.
  • Bake muffins in preheated oven for 24-26 minutes, or until a toothpick when inserted in comes out clean.
  • Let cool to room temperature and then serve. Enjoy!
Last step! If you make this, please leave a review letting us know how it was!

Tap stars to rate!

4.41 from 5 votes



Calories: 231kcal, Carbohydrates: 36g, Protein: 3g, Fat: 9g, Saturated Fat: 7g, Cholesterol: 19mg, Sodium: 250mg, Potassium: 61mg, Fiber: 3g, Sugar: 16g, Vitamin A: 2464IU, Vitamin C: 1mg, Calcium: 50mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Made this recipe?Leave a comment below!


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    1. Yes, Karen! You absolutely can use turbinado sugar in place of the coconut sugar. It might alter the taste and texture slightly, but they should still come out great! Would love to hear what you think 🙂

  1. 5 stars
    Good morning, I just made these and they turned out delicious. Only thing I changed was I used organic SunCoco oil. A sunflower & coconut oil blend. The texture is just like the real deal. Also, I love using King Arthur gluten free flour for my baking.

    1. What a great idea, Tammy! I have not tried the sunflower/coconut oil blend yet or the King Arthur blend. Always love new product suggestions! Thanks so much for your comment and rating 🙂

  2. Hi London,
    Wondering if I can use some Ancient Nutrition Pumpkin Spice flavor powdered bone broth in this recipe. They always say you can use it in all your recipes but I never know how it will affect the outcome. It has a strong pumpkin spice flavor.

    1. Hi Kathy! I have not personally ever tried the flavored bone broth but would love to know what you think! If you do use it, I would suggest altering the pumpkin pie spice accordingly. Thanks for the question!