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/ Last Modified On January 15, 2023High in fiber and potassium, these Gluten-Free Honey Flaxseed Muffins are the perfect breakfast to get your day started right. You are going to love these easy flaxseed muffins.
If you love enjoying healthy muffins you'll want to make my Paleo Pumpkin Muffins. They are healthy and perfect any time of year. My Gluten Free Blueberry Banana Muffins are also delicious.
Gluten Free Flaxseed Muffins
Tender, sweet, and loaded with super-foods like honey, flax seed, and bananas, these Gluten-Free Honey Flaxseed Muffins are our new go-to muffin. If you've read any of my other breakfast posts, you'll know that my kids won't eat cereal.
I'm not complaining. I LOVE that they want fresh baked muffins and homemade cereal for breakfast. Some of their favorites are my Paleo Chocolate Chip Muffins, and my Oat Flour Muffins.
Muffins like these honey flaxseed muffins can be a healthy and nutritious way to start the day.
Because they like homemade breakfasts it gives my husband and I more control over what they eat. We know exactly what they are putting into their growing bodies. We love these Gluten-Free Honey Flax Seed Muffins because of how nutritious they are.
They are naturally sweetened with honey, bananas, and applesauce. Each of which has vitamins and minerals their growing bodies need.
Is Flaxseed Gluten Free
I often get the question is flaxseed gluten free. Yes, it's a seed and it's nutritious. We often add flaxseed to recipes to get an extra boost of vitamins and fiber.
One of my favorite ways to use flaxseed is in these Paleo Chocolate Chip Cookies.
The combination of ingredients and flavors in these flaxseed muffins produce an incredible flavor and texture. You won't be able to tell that they are gluten-free. These honey flaxseed muffins store well at room temperature. They also freeze well. I've made a big batch of muffins and frozen half for the following week.
How to make flaxseed muffins
- Add ground flax seed, baking soda, baking powder, and salt to a medium mixing bowl.
- Mix until combined.
- In a separate medium mixing bowl, beat together egg, honey, oil, mashed banana, applesauce, and dairy-free milk.
- Add dry mixture to wet mixture.
- Sir just until blended.
- Spoon batter evenly into paper liners, filling about ⅔ full. Bake as directed.
These numbered steps match the numbered photos above and are for illustration purposes only. Please see the printable recipe card below.
Because these muffins already have ½ cup of flax seed, I would not recommend trying to use a flax-egg in place of the egg. I think it would throw the balance of the other ingredients off and come out too wet. If you try an egg replacer please leave me a comment below and let me know how it turned out and which one you used.
Did you make these gluten free honey flaxseed muffins? Please leave a comment below letting me know what you thought.
Gluten-Free Honey Flaxseed Muffins

High in fiber and potassium, these Gluten-Free Honey Flaxseed Muffins are the perfect breakfast to get your day started right.
Ingredients
- 1 1⁄2 cups gluten free flour blend (we've used Ryze yellow bag or Bob's Red Mill 1-to-1)
- ½ cup ground flax seeds
- 1 teaspoon baking soda
- 1 teaspoon gluten-free baking powder
- 1⁄2 teaspoon salt
- 1 large egg
- ½ cup honey
- ⅓ cup avocado oil
- 2 large overripe bananas, mashed
- ½ cup unsweetened applesauce
- ¼ cup dairy-free milk
Instructions
- Preheat oven to 350°F. Line a 12-serving muffin pan with liners; set aside.
- In a medium mixing bowl combine flour, ground flax seed, baking soda, baking powder, and salt.
- In a separate medium mixing bowl, beat together egg, honey, oil, mashed banana, applesauce, and dairy-free milk.
- Add dry mixture to wet mixture, and stir just till blended.
- Spoon batter evenly into paper liners, filling about ⅔ full.
- Bake for 20-22 minutes or until a wooden toothpick inserted near center comes out clean.
- Store leftover muffins in an airtight container at room temperature for up to two days.
Notes
- Make these muffins ahead of time and freeze them for an quick breakfast.
- Flour blends: We've used Ryze yellow bag or Bob's Red Mill 1-to-1 in this flaxseed muffin recipe.
- When measuring flour, spoon the gluten free flour into the measuring cup and then level it. Don't scoop the measuring cup into the flour.
- You can use your milk of choice.
Nutrition Information:
Yield:
12Serving Size:
1 muffinAmount Per Serving: Calories: 152Total Fat: 8gSaturated Fat: 1gTrans Fat: 0gUnsaturated Fat: 7gCholesterol: 16mgSodium: 245mgCarbohydrates: 20gFiber: 2gSugar: 15gProtein: 2g

Kaila (The Wanderlust Celiac)
These look and sound delicious. I tried a Ryze flour at the GFAF Expo, and really liked it!
Becky
Thank you so much for this recipe. I added cashews and walnuts. I doubled the recipe because these went so fast!
Kara
Can you leave out the flaxseed? If so, do you need to substitute something or can you omit it completely? Thanks
chrystal
Hi Kara,
The flaxseed plays a big role in these muffins. You can make these banana muffins instead if you like: https://www.glutenfreepalate.com/best-gluten-free-blueberry-banana-muffins/ - leave out the blueberries for a similar muffin but without the flaxseed.
Best,
Chrystal
Kelly
I love the use of flax in here. I'm always looking for more ways to use it!
Amanda
I'd love to have these warm with some honey drizzled. Muffins rule!
Lindsey
I'd love to try these. I'm sure I could substitute a flax egg and a different sweetener to make this vegan friendly.
Kortney
Love that your kids don't like cereal. Cereal is one of my weaknesses... I could eat a box in one sitting.
Leslie
I cannot think of a meal that these would not be perfect for! I'd have them for more than just breakfast.
K.C.
Do you remember that nursery song "Oh do you know the muffin man?" Well, I'm sure he never made any muffins as beautiful as these!
Jereann Zann
My kids want the homebaked breakfasts too! Muffins make life easier on busy mornings. Can't wait to try this recipe.
Alisa Fleming
I keep meaning to try that flour! I did a write up on it for Allergic Living, but had to go on someone else's notes on how it worked - they loved it! These muffins look fabulous, too - love the infusion of flax.
Megan
Yes to ALLLLL the flax things! Texture looks fabs.
Heather
What other types of gf could you recommend?
Heather
*gf flour
chrystal
Hi Heather,
You can use Bob's Red Mill 1-to-1 gluten-free flour, or gf jules in this recipe. I haven't tried other blends with this recipe, but the common ingredients between the blends is a combination of tapioca, potato, and rice. Hope that helps!
Best,
Chrystal
Liz Barton
I'm allergic to bananas and apples. Do you have a flax muffin recipe without those 2 ingredients? Thanks!
chrystal
I have a blueberry muffin recipe.
Best,
Chrystal
Heather
I have made these 2xs this summer for my 3 little ones and they are amazingly delicious and meet our gluten free lifestyle (Celiac disease). They love adding a little butter and homemade cherry jam. This recipe is a keeper. Thank you so much for sharing- makes this momma's heart happy!
chrystal
Hi Heather,
Thank you for stopping by and letting me know you like the recipe 🙂 So glad your little ones enjoy them.
Best,
Chrystal
Nicole
Can you use 2% milk for this recipe?
chrystal
Yes, you can use 2% milk.
Best,
Chrystal
Tayyaba
Just came across this recipe. Would love to try it but don't have apple sauce at home. Can I replace with something else??
chrystal
HI Tayyaba,
You might want to try another fruit puree or yogurt. Hope that helps. I haven't tested these myself but they are often substitutes for applesauce in muffins.
Best,
Chrystal
Bonnie
What can I substitute for avocado oil?
chrystal
Hi Bonnie,
You can use your oil of choice. I’ve used vegetable oil and melted and cooled coconut oil in this recipe as well.
Best,
Chrystal
Carly
How well would these freeze? It would take us at least 4-5 days to get through these as it’s just the two of us. I’d hate to wast any 🙁
chrystal
Hi Carly,
They freeze well. 🙂 Just make sure they are in an airtight container.
Best,
Chrystal
Shoba
Hi... can I use your flour blend for this recipe?
chrystal
Hi Shoba,
Yes, both of my blends work in this recipe.
Best,
Chrystal
Durga
Can I use coconut milk as dairy free milk?
chrystal
Yes, you can use coconut milk. It's best if you don't use full fat as it makes the batter too thick.
Best,
Chrystal
Nathaly Saucier livano
Do you have a replacement for the bananas? My youngest is allergic to bananas (I know it is crazy but he has lots of intolerances)...
chrystal
Hi Nathaly,
You can use 1 cup of pumpkin puree instead of the two bananas. You may have to adjust the cooking time. Make sure all the ingredients are at room temperature before you make the batter.
Best,
Chrystal
Victoria
I made these with coconut cream and they came out very moist and delicious. Wonderful smell as they are baking because of the banana. My house smells homey. Delicious recipe, thank you.
chrystal
I'm so glad you like them! Thank you for letting me know.
Best,
Chrystal
Samina
Hi Chrystal,
Could you please tell me the quantity of mashed bananas in cups needed to make these muffins?
chrystal
Hi Samina,
1 cup of mashed banana.
Best,
Chrystal
Samina
Hi Chrystal,
I tried these muffins and they were delicious!! Soft and moist with yummy bananas and perfect sweetness. I like how you use honey and maple syrup in your Paleo recipes so we gobble them up guilt free and also gluten and dairy free! These are delicious and healthy and much better than store bought muffins. I explore your site everyday so what to bake next
Thank you for developing such healthy and yummy recipes, I really appreciate it.
chrystal
You are very welcome. I am so glad you are enjoying my recipes.
Best,
Chrystal
Megan
I used Ener-G egg replacer (for 1 egg) to make this recipe, and it made a batch of great muffins with a proper crumb, and lovely, buttery taste. I used cashew milk, and fresh homemade baking powder (cream of tartar and baking soda). I added 1/2 tsp. cinnamon, and Enjoy Life mini chocolate chips to make the muffins extra-special. Thanks for a great recipe!
chrystal
You are very welcome. Thanks for sharing what you used!
Best,
Chrystal
Munira Shamim
Chrystal, These turned out to be moist, sweet, and simply delicious. Thank you!
PS: I used almond flour as my gluten-free flour.
pearlgem
Hi
Any idea if spelt flour would work in this recipe instead?
chrystal
I haven't worked with spelt flour in this recipe.
Best,
Chrystal
Char
I've been looking for a dairy free, gluten free, processed sugar free, high fiber raisin cereal for a year. This recipe is all that for me plus the convenience of eating it on the run. I didn't have bananas so I used 1 cup dairy free unsweetened almond yogurt plus a tablespoon of maple syrup and added a 1/2 cup of raisins. I also added 12 scoops of collagen powder to increase the protein content. Seriously so light and fluffy and delicious!
Side note: I forgot to add the baking powder and they still turned out amazing!!
Wendy Stoltz
Hi Char That sounds like a great modification to the recipe! I'm so glad to hear that it worked out well for you and that you could make it to fit your dietary needs. It's always great to find versatile recipes that can be customized to meet individual preferences. And it's great to know that the recipe turned out well even without the baking powder - sometimes happy accidents can lead to great results!