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You won't believe these delicious muffins are healthy! Yes, Healthy Pumpkin Chocolate Chip Muffins. I have them on repeat for breakfast and dessert! This clean eating recipe is made with whole grain flour and is naturally vegan (though standard baking alternates are included) #recipe #healthy #healthyrecipes #healthyfood #cleaneating #recipe #realfood #vegan #veganrecipe

Healthy Pumpkin Chocolate Chip Muffins Recipe | Whole Grain, No Refined Sugar, Vegan

  • Author: Diana of
  • Prep Time: 10 mins
  • Cook Time: 20 mins
  • Total Time: 30 mins
  • Yield: 12 1x


This Healthy Pumpkin Chocolate Chip Muffins Recipe is so delicious, you won’t believe it’s healthy. Made with whole grains, it’s also refined sugar free and vegan.


  • 2 cups spelt flour (or sub flour of choice)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1 1/2 teaspoons pumpkin pie spice (or sub cinnamon)
  • ¼ teaspoon salt
  • ½ cup chocolate chips (use vegan / no refined sugar to stay in line with the theme of this recipe)
  • 1 flaxseed egg (1 tablespoon ground flaxseed mixed with 3 tablespoons water – let sit for about 10 minutes) (or sub an egg if you want to make it non-vegan)
  • ½ cup coconut palm sugar (or sub sugar of choice)
  • 1 ½ cups canned pumpkin
  • 1/2 cup almond milk (or sub milk of choice)
  • 3 tablespoons canola oil (or other oil of choice)
  • 1 teaspoon vanilla extract


  1. Pre-heat oven to 350 degrees F and prepare a 12 cup muffin tin with non-stick spray or muffin liners.
  2. In a large bowl, prepare the flaxseed egg.
  3. Add spelt flour, baking powder, baking soda, and pumpkin pie spice into a medium bowl and whisk together. Add chocolate chips and whisk in.
  4. In the wet ingredient bowl, add coconut sugar and whisk to the flaxseed egg till combined.
  5. Whisk in pumpkin, almond milk, canola oil, and vanilla extract.
  6. Pour dry ingredient mixture into the wet ingredient mixture, and stir gently just to combine – careful to not over-mix.
  7. Pour/spoon muffin batter into muffin cups – about ¾ full each. Use spatula to flatten tops if needed. This batter is SUPER thick, guys.
  8. Bake for 18-22 minutes until centers set or a toothpick inserted in the center of a muffin comes out clean.
  9. Cool at least 10-15 minutes, or until safe to eat, before serving. Enjoy!


Pumpkin makes this batter really-really dense. It may take some extra time to bake and you may notice a toothpick inserted into the middle comes out sticky for a bit. This is expected but once it comes out clean, you’ll have a super moist and tender muffin. For comparison, I baked mine for 21 minutes total (16 + 3 + 2 with two toothpick checks). It may take a little less time for you if you don’t open the oven door twice like I did.

If you prefer to use or only have 1 cup of pumpkin, you can use that but you must also increase the total almond milk used to 3/4 cup total (which is 1/2 more than the original recipe used).

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