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

basket of gluten-free flax muffins ready to enjoy.

These healthy flax muffins are surprisingly light and fluffy! They have a neutral flavor with just a touch of sweetness, plus they have great texture.

Whether you’re looking to add more fiber to your diet or you just want to eat more flax, then these muffins are for you. Flax has been studied for its unique nutritional properties, and has research showing many health benefits.

Why You Need This Recipe

  • This recipe is actually really easy to make. And, these Gluten-Free Flax Muffins are super healthy with fiber and wholesome ingredients.
  • This recipe is gluten-free and dairy-free. Serve these yummy breakfast muffins warm out of the muffin pan. Or, prep them ahead of time and grab one as an easy breakfast or snack.
  • You can adapt this recipe to be paleo if need be. Just use almond flour instead of a gluten-free flour blend.

Key Ingredients

Ingredients to make flax muffins in small bowls on a white surface.

Ground flax makes the base of these muffins. You can either buy ground flax seed in a bag, or buy whole flax seeds and grind them yourself in a Vitamix blender.

You’ll also need basic baking ingredients including a gluten-free flour blend (I use and recommend the Bob’s 1-to-1 Gluten-Free Baking Flour). Substitute almond flour to make these gluten-free muffins paleo and grain-free too.

Sugar helps sweeten the muffins. You can use white sugar, coconut sugar, date sugar, or brown sugar.

Cinnamon helps add depth of flavor to the muffins.

You’ll also need a neutral-flavored oil like melted coconut oil or olive oil for the muffins.

Recipe Steps

Process collage of mixing up gluten free flax muffins.

Step One

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

Then, in a large mixing bowl, you just combine the dry ingredients including the ground flaxseed, flour mixture, baking powder, and coconut sugar.

Step Two

Add the wet ingredients into the dry ingredients.

Step Three

Stir the ingredients until combined.

Step Four

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

Bake the muffins for about 20 minutes, or until the tops have turned a golden brown. Let them cool on a wire rack before serving.

These Cinnamon Flax Muffins are such a great healthy grab-and-go breakfast, or a healthy snack or dessert! Serve them warm or at room temperature.

Muffin tray filled with baked flax muffins.

Recipe Tips & Substitutions

  • You can freeze any leftover muffins in a zip top bag for up to 2 months. Defrost in the refrigerator overnight before consuming.
  • If you aren’t gluten-free, you can use regular whole wheat all-purpose flour. You can also use almond flour or oat flour instead of the gluten-free baking mix, if you prefer.
  • Use any milk you’d like, including cows’ milk if you aren’t dairy-free.
  • Want an apple version? Try these Gluten-Free Vegan Applesauce Muffins.

Recipe FAQs

Can I use whole flaxseeds in this recipe?

No, you need to use ground flax, not whole flaxseeds.

Does flax affect female hormones?

Flax contains lignans which are phytoestrogens. Some studies have shown that consumption of flax can affect female hormone levels.

Can I use maple syrup to sweeten these muffins?

I tested the recipe using a dry sweetener. I have not tested this recipe using a liquid sweetener.

Flax muffin split open on a small white plate.

More 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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Flax muffins and cinnamon sticks out on a white counter.

Gluten-Free Flax Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

5 from 7 reviews

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

  • Total Time: 35 minutes
  • Yield: 12 1x

Ingredients

Units Scale
  • Nonstick cooking spray
  • 1/2 cup ground flax seed
  • 1 1/4 cups gluten-free baking flour (I used Bob’s 1-to-1 Gluten-Free Baking Flour)
  • 1 tablespoon baking powder
  • 3 tablespoons coconut sugar or cane sugar
  • 2 teaspoons ground cinnamon
  • 1/4 teaspoon sea salt
  • 1/4 cup coconut oil, melted
  • 2 eggs, lightly beaten
  • 1/2 cup unsweetened almond milk (you can use regular dairy milk if you aren’t on a dairy-free diet)

Instructions

  1. Preheat oven to 350°F.
  2. Spray a muffin tin lightly with nonstick cooking spray and set aside.
  3. Combine the ground flaxseed, flour, baking powder, coconut sugar, cinnamon, and sea salt into a large mixing bowl and whisk together.
  4. Next, add the coconut oil, 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 18-22 minutes or until the muffins have turned a golden brown and a toothpick inserted into the center of one comes out clean.
  6. Remove each muffin from the tin and let them cool slightly on a rack before serving.

Notes

  1. You can freeze any leftover muffins in a zip top bag for up to 2 months. Defrost in the refrigerator overnight before consuming.
  2. If you aren’t gluten-free, you can use regular whole wheat all-purpose flour. You can also use almond flour or oat flour instead of the gluten-free baking mix, if you prefer.
  3. Use any milk you’d like, including cows’ milk if you aren’t dairy-free.

Nutrition

  • Serving Size:
  • Calories: 172
  • Sugar: 3.2 g
  • Sodium: 74.2 mg
  • Fat: 9.4 g
  • Saturated Fat: 4.4 g
  • Carbohydrates: 19.2 g
  • Fiber: 3.2 g
  • Protein: 3.7 g
  • Cholesterol: 31 mg

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About the Author: Carrie Forrest has a master’s degree in public health with a specialty in nutrition. She is a top wellness and food blogger with nearly 10 million annual visitors to her site. Carrie has an incredible story of recovery from chronic illness and is passionate about helping other women transform their health. Send Carrie a message through her contact form.