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Gluten-Free Flax Seed Muffins

Gluten-free muffins with flax seeds incorporate homemade flax seed meal, gluten-free flour, and an apple puree.

  • Total Time:
  • Servings: 6

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  • 2 medium apples
  • 1 1/2 cups all-purpose gluten-free flour
  • 1 1/2 cups flax seed meal (See Note)
  • 1 cup brown sugar
  • 2 teaspoons baking soda
  • 2 teaspoons cinnamon
  • 1 teaspoon kosher salt
  • 2 large eggs, lightly beaten
  • 3/4 whole milk or unsweetened almond milk
  • 1 teaspoons vanilla extract
  • 1/4 cup whole flax seeds


  1. Preheat the oven to 350º. Peel and puree the apples in a blender or food processor. Set aside (the mixture will turn brown). Line a 6-muffin tin with large paper cups, and set aside.
  2. In a large bowl, mix the flour, flax seed meal, sugar, baking soda, baking powder, salt, and cinnamon. In a separate bowl, combine the milk, eggs, and vanilla. Mix well, and slowly pour the liquid ingredients into the dry ingredients, stirring. When the wet and dry ingredients are combined, add the apple puree and and stir to combine.
  3. Using a measuring cup or scoop, evenly divide the batter between the muffin cups. (They will fill nearly all the way to the top, and because these are gluten-free muffins, they aren't going to rise too much.) Sprinkle the flax seeds on top of each muffin. Bake, uncovered, for 20-30 minutes or until a toothpick inserted in the center of the muffin comes out clean. Cool in the muffin tin for 5 to 10 minutes.

Make Ahead

Muffins will keep in an airtight container for 3 days.


Because store-bought flax seed meal lacks the nutritional value of whole flax seeds, it's best to make a fresh, coarse-ground flax seed meal just before you use it. Flax seed meal is easy to make with a with a food processor, clean coffee grinder, or blender. One cup of whole flax seeds yields about 1 2/3 cups of flax seed meal, so leave room for expansion (use any leftover flax seed meal in smoothies or sprinkled on top of cereal or yogurt).

Contributed By Photo © Emily Farris

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