Healthy Pumpkin Chocolate Chip Muffins {gluten free & low sugar}

Pumpkin Desserts & Baked Goods

Enjoy the taste of fall with these healthy pumpkin chocolate chip muffins that are gluten free and low in sugar. They are super moist and pumpkin-y!

There’s truly nothing better than pumpkin muffins cooking in the oven and the smell filling your house on a cozy fall day. These pumpkin chocolate chip muffins will do just that and make you feel all the fall feels upon first bite!

healthy pumpkin chocolate chip muffins

If you follow me on Instagram then you know I enjoy my fair share of pumpkin treats all fall long. Since I’m always baking something up, I like to keep all of my sweeter pumpkin recipes lower in sugar, and higher in nutritious ingredients like oat flour, almond flour and maple syrup.

Nutrient Benefits of These Pumpkin Chocolate Chip Muffins

Low in sugar, and high in fiber from the pumpkin puree and oat flour, this muffin recipe will turn into one of your favorites to make all fall long!

Pumpkin itself is a super nutritious and versatile vegetable. It adds vitamin A, C, E potassium and fiber to anything to add it too. It’s texture also makes soups and smoothies thick and creamy.

What to Pair With These Muffins

My favorite way to eat these healthy pumpkin chocolate chip muffins is warmed up with a little drizzle of peanut butter, or better yet, pumpkin spice peanut butter on top!

I used Lily’s semi-sweet baking chocolate chips in this recipe and I love how they taste in any pumpkin baked good!

pumpkin chocolate chip muffins

Ingredients Needed for Healthy Pumpkin Chocolate Chip Muffins

  • Gluten free oat flour
  • almond flour
  • pumpkin puree
  • maple syrup
  • coconut oil
  • 1 egg
  • vanilla
  • pumpkin pie spice
  • baking soda
  • baking powder
  • salt
  • chocolate chips

Do you love all things pumpkin spice in the fall like I do? Check out this list of the 26 best pumpkin spice foods to satisfy your PSL cravings that I contributed to in Women’s Health.

pumpkin chocolate chip muffins
healthy pumpkin chocolate chip muffins

Healthy Pumpkin Chocolate Chip Muffins {gluten free & low sugar}

Maggie Michalczyk, RDN
Take a bite out of fall with these healthy pumpkin chocolate chip muffins! Super fluffy, and moist, these muffins are perfect when the weather starts getting chilly and you’re craving all things pumpkin! 
Prep Time 10 minutes
Cook Time 25 minutes
Servings 12 muffins


  • Wet Ingredients
  • 1 cup 100% pure pumpkin puree
  • ¼ cup melted coconut oil
  • ¼ cup pure maple syrup
  • 1 egg
  • 1 tsp. vanilla extract
  • Dry Ingredients
  • 2 cups gluten free oat flour*
  • ½ cup blanched almond flour
  • 1 tsp. baking soda
  • ½ tsp. baking powder
  • 2 tsp pumpkin pie spice
  • ¼ tsp salt
  • sprinkle of nutmeg
  • 3/4 cup semi-sweet chocolate chips I love this brand!


  • 1. Preheat oven to 350°F. Line a muffin tin with liners and spray the liners with coconut oil or cooking spray so that the muffins come out easily.
  • 2. Add the wet ingredients to a large bowl: pumpkin, coconut oil, maple syrup, egg, and vanilla. Whisk until well incorporated.
  • 3. Add the dry ingredients to a medium sized bowl. Whisk together until just incorporated, and add the wet ingredients to the dry. Mix until just combined, careful not to over mix. Fold in chocolate chips.
  • 4. Pour batter evenly into the prepared muffin pan. I used a cookie scoop to portion them all evenly. Sprinkle a few extra chocolate chips on top of each muffin. Bake for 20-25 minutes.
  • 5. Transfer to a cooling rack, and let cool. Store in an airtight container in the fridge for up to a week or freeze. 


*You can buy oat flour or make your own by pulsing old fashioned oats in the food processor. 
Keyword pumpkin chocolate chip muffins

If you like this pumpkin muffin recipe, I know you will love these other pumpkin filled recipes perfect for fall!

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pumpkin chocolate chip muffins
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