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3 Seed Pumpkin Muffins

best vegan pumpkin muffins

Does anyone need another pumpkin muffin recipe? Probably not. But this one’s different. A bit seedier.

Pumpkin hooks up with sunflower and chia seeds in a barely sweet vegan muffin. If you haven’t played with chia seeds yet, you’re missing out. They’re so versatile. I LOVE my morning chia smoothie. Sounds overly possessive, but there you are.

Chia seeds mixed with apple cider (or any liquid) form a gel that performs double duty.  No eggs or xanthan in this recipe, but there’s loads of pumpkin spice flavor. Equally delicious for breakfast or dessert, these gluten free pumpkin muffins are moist, flavorful, and great to have on hand for a quick snack.

3 Seed Pumpkin Muffins

24 minutes

12 muffins

Healthy pumpkin muffins with chia, pumpkin, and sunflower seeds! Mixes up easily by hand in about 10 minutes.


  • 1 tablespoon chia seeds in 1/4 cup apple cider
  • 1 1/2 cups gluten free flour (see notes)
  • 1/2 cup sugar (raw, coconut, whatever you like)
  • 2 teaspoons baking powder
  • 1/2 teaspoon cinnamon
  • 1/4 teaspoon each: ginger and nutmeg
  • 1/4 teaspoon salt
  • 1/4 teaspoon baking soda
  • 3/4 cup pumpkin puree
  • 1/2 cup milk (coconut or hemp)
  • 1/3 cup olive oil
  • 1 tablespoon pure vanilla extract
  • 1/2 teaspoon apple cider vinegar, optional
  • 1/4 cup pumpkin seeds
  • 1/4 cup sunflower seeds


Preheat oven to 350 degrees. Place 12 paper liners in cupcake pan. Add chia seeds to apple cider and stir. Set aside.

In a medium bowl, combine: gf flour, sugar, baking powder, cinnamon, ginger, nutmeg, salt, and baking soda. In a separate cup, blend pumpkin, milk, oil, chia mixture, pure vanilla extract, and vinegar. Add liquid ingredients to dry ingredients and stir thoroughly.

Fill paper lined muffin tins with batter using a number 16 disher to scoop batter evenly. Sprinkle tops of muffins with pumpkin and sunflower seeds before baking.

Bake for 24-25 minutes, until tester inserted remains mostly clean.


I've used a rice flour blend and sorghum bread blend with good results. Feel free to use your favorite gf all purpose blend. Find more on blending gf flours here.

Extra muffins can be stored frozen to defrost as needed.

Muffins will be a bit fluffier made with vinegar, but are still delicious without . . .


3 seed pumpkin muffins vegan recipe

Hungry for more? Check out what’s cooking at Gluten Free Wednesdays!


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