Flavorful and moist pumpkin muffins are made healthier with whole wheat flour, coconut oil, and honey! Healthy Pumpkin MuffinsJust when you thought pumpkin season couldn’t get any better, along came these healthy pumpkin muffins. They’re full of pumpkin and spice flavor and are everything full should be.

They’re made healthier by using healthy flour, oil, and sugar alternatives and are so delicious you would never know! They make a delicious grab and go breakfast or snack and are kid-approved too. 

To Make Healthier Pumpkin Muffins You Will Need:

There are a few substitutions you can make with this recipe that will yield about the same results and help keep these muffins healthy.


  • White whole wheat flour
  • Whole wheat flour
  • A mixture of 1:1 All-purpose flour and whole wheat flour
  • Oat flour; old fashion oats blended in the blender until they reach a flour consistency.


  • Honey
  • Maple Syrup
  • coconut sugar


  • Coconut oil
  • almond butter
  • apple sauce
  • butter


  • Any type of Cow’s Milk
  • Any type of nut milk
  • Greek yogurt
  • Sour-cream


  • dark chocolate chips or chunks
  • chopped nuts
  • raisins

To Make Vegan Pumpkin Muffins

Replace the eggs with flax eggs and the milk with almond milk.

3.20 from 5 votes

Healthy Pumpkin Muffins

Moist and flavorful pumpkin spice muffins are healthy and make a delicious breakfast. They're sugar-free and made with whole wheat flour, coconut oil. and maple syrup. 
Prep10 minutes
Cook25 minutes
Total35 minutes
Servings 12 muffins


Dry Ingredients:


  • Preheat oven to 350 degrees F. Line a 12 cup muffin tin with liners or lightly grease pan with cooking spray or butter. 
  • In a large bowl whish the flour, pumpkin spice, and baking soda; set aside. 
  • In another large bowl, whisk the pumpkin puree, eggs, honey, oil, milk, and vanilla until combined. Add the flour mixture to the wet ingredients and mix until fully combined. Fold in your favorite add-ins if desired. 
  • Divide batter into 12 muffin cups. Bake for 25 minutes or until a tester comes out clean. 



Please see above for a full list of substitutions*
White whole wheat flour can be ordered from Amazon or purchased from Trader Joe's (Under $3). 


Serving: 1muffin, Calories: 210kcal, Carbohydrates: 28g, Protein: 3g, Fat: 10g, Saturated Fat: 8g, Cholesterol: 27mg, Sodium: 120mg, Potassium: 89mg, Fiber: 2g, Sugar: 17g, Vitamin A: 3225IU, Vitamin C: 0.9mg, Calcium: 32mg, Iron: 0.9mg

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

Additional Info

Course: Snack
Cuisine: American
Keyword: cupcakes, healthy, muffins, pumpkin
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  1. (I think you forgot to list the sugar in 2. of the instructions.)

    Looks nice! I’m going to try it with sweet potato, which I have at home.
    I’m going to cut way down on the sugar, and the oil.

  2. Can you use pumpkin pie mix instead of pureed pumpkin?

    1. I would not recommend pumpkin mix as it has added sugars and spices.

  3. Can you use canned ‘pure’ pumpkin instead of pureed pumpkin?