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Two pumpkin muffins stacked on top of each other. They are balancing on top of a baking tin.
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4 from 51 votes

Healthy Pumpkin Muffins

These healthy pumpkin muffins are naturally sweetened and made with whole wheat pastry flour, rolled oats, yogurt and fall spices. They're perfectly moist and fluffy and come together quickly.
Prep Time10 minutes
Cook Time22 minutes
Total Time32 minutes
Course: Breakfast
Cuisine: American
Keyword: healthy pumpkin muffins
Servings: 12



  • Preheat oven to 350°F. Line a muffin tin with silicone or paper liners.
  • Whisk together the pumpkin puree, honey, greek yogurt, oil, eggs and vanilla in a large bowl.
    Pumpkin puree, honey, greek yogurt, oil, eggs and vanilla whisked together in a mixing bowl.
  • Combine the flour, oats, pumpkin pie spice, baking soda and salt in a medium mixing bowl.
    Flour, oats, pumpkin pie spice, baking soda and salt in a medium mixing bowl.
  • Add the dry ingredients into the bowl with the wet ingredients and mix until just combined. There may be a few lumps, that’s totally fine. Just don’t over mix!
    Wet and dry ingredients combine in a mixing bowl. A spoon is sticking out of the mixture and bowl.
  • Divide the batter evenly between muffin cups. Sprinkle a few oats on the tops of each muffin.
    Pumpkin muffin battered divided between 2 6-muffin tins lined with brown cupcake liners.
  • Bake muffins for 22 to 24 minutes, or until a toothpick inserted into a muffin comes out clean.
    12 freshly baked muffins still in baking tins.
  • Place the muffin tin on a cooling rack to cool. Once cool enough to handle, remove from the muffin tin and to cool completely.
  • They’ll keep at room temperature for up to 2-3 days, or in the refrigerator for 4-5 days. They keep well in the freezer in a freezer-safe container for up to 3 months.


  • We tested this with ½ cup of maple syrup and then with ¾ cup honey. We liked the honey version much better, but if you want the muffins less sweet, feel free to reduce the sweetener to ½ cup.
  • Need this recipe to be gluten-free? You should be able to swap a gluten-free all purpose blend for the whole wheat pastry flour or try this tested and approved flourless pumpkin muffin recipe!
  • Need a vegan recipe? Try my vegan pumpkin muffins instead!
  • Optional mix-ins: You could add some chopped nuts, chocolate chips or dried cranberries to the batter.


Serving: 1muffin | Calories: 204kcal | Carbohydrates: 40g | Protein: 5g | Fat: 4g | Saturated Fat: 1g | Monounsaturated Fat: 2g | Cholesterol: 31mg | Sodium: 187mg | Potassium: 23mg | Fiber: 4g | Sugar: 18g