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gluten free pumpkin muffins on table.

Gluten-Free Pumpkin Muffins with Chocolate Chips

These delicious Gluten-Free Pumpkin Muffins with Chocolate Chips are a great healthy snack or dessert. They include pure pumpkin puree along with other fall flavors. Make a batch of these yummy muffins today! This recipe is also dairy-free and vegan-friendly.

  • Total Time: 40 minutes
  • Yield: 12 1x


Units Scale
  • Nonstick cooking spray
  • 2 eggs, beaten (use flax eggs for vegan)*
  • 1 cup pumpkin puree
  • 1/4 cup neutral-flavored oil (I used avocado oil)
  • 1/4 cup unsweetened almond milk
  • 1 1/2 cups gluten-free flour (I used Bob’s Red Mill 1 to 1 Gluten-Free Baking Mix)
  • 1/2 cup coconut sugar or white sugar
  • 3/4 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1 teaspoon pumpkin pie spice
  • 1/4 teaspoon sea salt
  • 3/4 cup chocolate chips, divided into 1/2 cup and 1/4 cup


  1. Preheat your oven to 400°F. Spray a muffin tin with nonstick cooking spray and set aside. 
  2. In a medium mixing bowl, combine the eggs, pumpkin puree, oil, and almond milk. Stir to combine.
  3. In a large mixing bowl, combine the flour, sugar, baking powder, baking soda, pumpkin pie spice, salt, and ½ cup of the chocolate chips. Stir to combine.
  4. Pour the wet mixture into the dry mixture and stir to combine.
  5. Divide the batter between the muffin wells and top the rest of the muffins with the remaining ¼ cup of chocolate chips.
  6. Bake for 25 minutes. Let the muffins cool for about 10 minutes before removing from the muffin tin.
  7. Serve warm or at room temperature.


  1. Be sure to use canned pumpkin that is 100% pumpkin with no other ingredients.
  2. If you want to freeze these muffins after they have baked, let them cool completely. Place them in a zip-top bag and freeze for up to 2 months.
  3. VEGAN: use two flax eggs in place of regular eggs. To make 2 flax eggs, combine 2 tablespoons of ground flax with 6 tablespoons of water. Let the mixture set for 10 minutes before using.
  4. If you don’t have pumpkin pie spice, you can use ground cinnamon instead.

Keywords: gluten free muffins, vegan pumpkin muffins, pumpkin spice