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three pumpkin chocolate chip muffins stacked on top of each other

Healthy Pumpkin Chocolate Chip Muffins

  • Author: Jessica Hoffman
  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x
  • Category: Dessert, Breakfast
  • Method: Bake
  • Cuisine: American
  • Diet: Vegetarian


The perfect fall muffin loaded with pumpkin, pumpkin spice and chocolate chips!


Units Scale
  • 1 3/4 cup spelt flour (can sub 1-1 gluten-free flour blend, or regular flour)
  • 1/2 cup organic cane sugar or coconut sugar
  • 3/4 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp salt
  • 2 tsp pumpkin spice
  • 1 cup pumpkin puree
  • 1/4 cup+ 2 tbsp apple cider (can sub orange juice or milk of choice)
  • 2 eggs
  • 1/3 cup coconut oil, melted and cooled
  • 1 tsp vanilla extract
  • 1/2 cup chocolate chips


  1. Preheat the oven to 350 degrees F, line a muffin pan with muffin liners and spray them with cooking spray to prevent any sticking. 
  2. Mix all the dry ingredients together in a large mixing bowl, and the wet ingredients together in a separate mixing bowl.
  3. Pour the wet ingredients into the dry and gently fold together until combined. Don’t overmix. 
  4. Add the chocolate chips and mix together just until combined. 
  5. Spoon the batter in the muffin pan filling each mould 3/4 of the way full. 
  6. Bake for 20-22 minutes or until a toothpick comes out clean. 
  7. Let cool for at least 15 minutes before eating.


Make sure to use pumpkin puree and not pumpkin pie filling! The only ingredient on the can should be pumpkin. 

Don’t overmix the batter. This is result in a dense and less fluffy muffin. Use a spatula to just gently fold the ingredients together. 

Don’t fill the muffin moulds all the way to the top. This can cause the batter to overflow. 


  • Serving Size: 1 muffin
  • Calories: 190
  • Sugar: 12g
  • Sodium: 160mg
  • Fat: 8g
  • Saturated Fat: 6g
  • Carbohydrates: 28g
  • Fiber: 2g
  • Protein: 4g

Keywords: healthy pumpkin muffins, pumpkin muffins with chocolate chips, chocolate chip pumpkin muffins healthy