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healthy pumpkin muffin cut open with chocolate chips

Healthy Pumpkin Muffins with Whole Wheat Flour

Healthy Pumpkin Muffins with Whole Wheat Flour are a perfect fall dessert, breakfast or snack. They are sweetened with honey (no white sugar), made in one bowl and so fluffy!
5 from 2 votes
Prep Time 8 mins
Cook Time 25 mins
Course Breakfast, Dessert, Snack
Cuisine American
Servings 10 muffins



  • Whisk together pumpkin, eggs, avocado oil and honey.
  • Add in whole wheat flour, almond flour, baking powder, pumpkin pie spice and chocolate chips. Mix until combined. Do not over mix.
  • Line a muffin tin with 10 liners. Use a large cookie scoop and scoop the batter into each muffin liner. Bake at 350 degrees F for about 20-25 minutes or until a toothpick comes out clean.
  • Let the muffins cool completely before enjoying!


How to measure flour correctly?
Spoon the flour into the measuring cup. Then, level off the top of the cup with a knife. Do not place the measuring cup into the bag and scoop. You could end up with more flour than needed.
What If I don't have pumpkin pie spice?
Combine cinnamon, ginger, allspice, cloves and nutmeg.
How to store healthy pumpkin muffins?
Store in an airtight container at room temperature and enjoy within 1-2 days. 
Store in an airtight container in the fridge and enjoy within about 3 days. 
To freeze, wrap each individual muffin in plastic wrap. Place the muffins into a freezer bag. Keep in the freezer for up to 3 months.
Keyword pumpkin muffins
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