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

Course Breakfast, Snack
Cuisine American
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Servings 12
Calories 129 kcal
Author Lindsey Janeiro, RDN, LDN


Wet Ingredients

  • 1 cup pumpkin puree
  • 1/4 cup avocado oil (or other neutral oil)
  • 1/4 cup unsweetened applesauce
  • 1/4 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
  • 1/2 tsp baking soda
  • 1/4 tsp salt

Optional Mix-In Ingredients:

  • 1/2 cup chocolate chips
  • 1/2 cup dried fruit (like raisins or dried cranberries)
  • 1/2 cup seeds or chopped nuts
  • 1/2 cup any combination of the above
  • cinnamon to sprinkle on top


  1. Preheat oven to 350F. Prepare a muffin tin by lightly coating each tin with non-stick spray.

  2. Whisk together wet ingredients in a large bowl. Stir in dry ingredients and any optional mix-in ingredients.

  3. 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).

  4. 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.

Recipe Notes

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.

Nutrition Facts
Healthy, Gluten-Free Pumpkin Muffins
Amount Per Serving
Calories 129 Calories from Fat 54
% Daily Value*
Fat 6g9%
Saturated Fat 1g6%
Cholesterol 27mg9%
Sodium 114mg5%
Potassium 104mg3%
Carbohydrates 18g6%
Fiber 2g8%
Sugar 6g7%
Protein 3g6%
Vitamin A 3217IU64%
Vitamin C 1mg1%
Calcium 42mg4%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.