Healthy Pumpkin Muffins in a basket with a dark napkin.

The Best Healthy Pumpkin Muffins

Cozy up for fall and treat your family to these healthy pumpkin muffins. They really are the best and use an entire can of pumpkin (no leftovers!).
Course Breakfast, Snack
Cuisine American
Prep Time 20 minutes
Cook Time 20 minutes
Total Time 40 minutes
Servings 12 muffins
Calories 120kcal
Author Nora Rusev



Dry Ingredients

  • 1 1/3 cups whole wheat flour
  • 1/4 cup brown sugar optional
  • 2 tablespoons cornstarch
  • 1 tablespoon pumpkin pie spice
  • 1 teaspoon baking powder
  • 1/4 teaspoon baking soda
  • 1/4 teaspoon salt

Wet Ingredients

  • 2 large eggs
  • 1 15- oz can pumpkin
  • 1/2 cup runny honey
  • 1 teaspoon vanilla extract


  • Prep: Preheat your oven to 330°F. Line a 12 cup muffin tin with nonstick muffin liners.
  • Combine ingredients separately: Whisk together all dry ingredients in a large bowl. In a separate measuring jug, whisk together all wet ingredients.
  • Make the batter: Pour the wet ingredients into the bowl with the dry ingredients. Fold just until combined, do not overmix. The batter will be quite thick.
  • Add to muffin pan: Evenly distribute the muffin batter between the prepared muffin cups (I find it works out the neatest if I do this with a large cookie scoop). Add streusel, if desired.
  • Bake the muffins: Bake in the preheated oven for 23-25 minutes, or until a toothpick inserted into the middle of a muffin comes out just clean.


The brown sugar is optional for a little sweeter and more decadent holiday treat. The muffins taste wonderful without it, too. (Nutrition facts are without sugar.)
I added the topping on a whim when I made these for the blog, because they look a little plain on photos without it. Combine 3 tablespoons quick cooking oats, 1 tablespoon chopped walnuts or pecans and 1/2 teaspoon pumpkin pie spice in a medium bowl. Cut in 2-3 tablespoons stick butter and mix with your fingertips until small crumbs form. Sprinkle over the muffins just before baking, slightly pressing it into the batter to help it stick.


Calories: 120kcal | Carbohydrates: 26g | Protein: 3g | Fat: 1g | Saturated Fat: 1g | Cholesterol: 27mg | Sodium: 85mg | Potassium: 181mg | Fiber: 3g | Sugar: 13g | Vitamin A: 5922IU | Vitamin C: 2mg | Calcium: 37mg | Iron: 1mg