These Gluten-Free Cinnamon Flax Muffins are such a healthy and delicious way to start the day. They are light and fluffy, with great texture and flavor. 

flax muffins on a cooling rack

These healthy flax muffins have a really wonderful texture. This recipe also includes some healthy baking tricks to cut back on the fat and increase the health-promoting qualities of these flax muffins.

Specifically, I’ve replaced half the oil with applesauce or squash puree. It’s such an easy swap that adds nutrition and fiber, and you likely won’t even notice the difference.

Another one of my healthy baking tips is to cut back on the grains, and use a grain-free option like flax meal, cassava flour, or almond flour instead. 

gluten free muffin ingredients on a cookie sheet

Recipe Highlights

This recipe is actually really easy to make! And, these Gluten-Free Flax Muffins are super healthy. Each flax muffin has approximately:

  • 160 calories
  • 4 grams of fiber
  • 4 grams of protein
  • and 13% of the recommended intake of magnesium

This recipe is gluten-free, grain-free (when made using almond flour), and dairy-free. This recipe can also be made vegan using an egg replacer.

Flax has been studied for its unique nutritional properties, and has research showing many health benefits.

Recipe Steps

Step One

The first step to making these healthy flax muffins is to gather up all the ingredients.

Then, you just combine the dry ingredients including the flax, flour, baking powder, coconut sugar, raisins, and cinnamon, and then add the wet ingredients.

muffin batter in a bowl

Step Two

Spray your muffin tin with non-stick cooking spray and then divide the batter between all the wells.

muffin batter in the muffin tin ready to be baked

Step Three

Bake your muffins for 30 minutes in a 375°F degree oven, or until the tops are golden brown. Serve warm.

cinnamon flax muffins cooling on a cooling rack

These Cinnamon Flax Muffins are such a great healthy grab-and-go breakfast, or a healthy snack or dessert!

muffins on small serving plates ready to be eaten

Other Healthy Gluten Free Muffin Recipes You Might Like

I hope you make this recipe! If you do, please leave a comment and a starred review below.

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gluten free muffins on a plate ready to serve

Cinnamon Flax Muffins


These Gluten Free Cinnamon Flax Muffins are such a healthy and delicious way to start the day. They are light and fluffy, with great texture and flavor. 


  • Nonstick cooking spray
  • 1 ½ cups ground flax seed
  • ½ cup almond flour or your favorite gluten-free flour
  • 1 teaspoon ground cinnamon
  • 2 teaspoons baking powder
  • 1/2 cup coconut sugar
  • 1/3 cup raisins
  • 1/4 cup coconut oil, melted
  • 1/4 cup butternut squash puree, pumpkin puree, or unsweetened applesauce
  • 2 eggs, beaten (for vegan, use the equivalent egg replacer)
  • 1/2 cup unsweetened almond milk


  1. Preheat oven to 375°F.
  2. Spray a muffin tin with nonstick cooking spray and set aside.
  3. Combine the ground flaxseed, flour, cinnamon, baking powder, coconut sugar, and raisins into a large mixing bowl and whisk together.
  4. Next, add the coconut oil, squash puree or applesauce, eggs, and almond milk to the mixing bowl and use a large spatula to stir together. Use a big spoon or measuring cup to divide the batter into the muffin tin.
  5. Bake for 30 minutes or until the muffins have turned a golden brown.
  6. Remove each muffin from the tin and let them cool slightly on a rack before serving.


You can freeze any leftover muffins in a zip top bag for up to 2 months. Defrost in the refrigerator overnight before consuming.

  • Category: Dessert
  • Method: Baking
  • Cuisine: Healthy

Keywords: flax muffins, gluten free flax muffins, healthy muffins

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