Flaxseed Muffins

Flaxseed muffins are a tasty way to add flaxseed into your diet! Packed with wholesome ingredients, flaxseed muffins are a recipe the whole family will enjoy. This recipe is gluten free, dairy free, vegetarian, and DELICIOUS.

Flaxseed muffins are a tasty way to add flaxseed into your diet! Packed with wholesome ingredients, flaxseed muffins are a recipe the whole family will enjoy. This recipe is gluten free, dairy free, vegetarian, and DELICIOUS.

***Please note that all our recipe posts contain detailed information about how to make the recipe so you achieve great results – this is not your average blog post and doesn’t include stories or other info you don’t need! We have made it easy to find the sections you need and skip the ones you don’t by using headings. 

Finally, a healthy muffin that tastes great! These flax muffins are made with wholesome ingredients and are gluten free, dairy free, and easy to make.

What is flaxseed?

Flaxseed is a nutritional powerhouse with many health benefits. is a good source of dietary fiber, protein, and iron. Just 2 tablespoons of ground flaxseed packs 11% of your daily fiber requirement, 3 grams of protein, 6% of your daily iron intake, plus some healthy omega 3’s.

According to the Mayo Clinic, most nutritional experts agree that ground flax seed provides more benefits than whole flax seeds because it is more easily digested.

Ground flaxseed can improve digestive health and may lower blood cholesterol levels, making it a great addition to you diet! Because flaxseed absorbs liquid, you’ll want to be sure you drink plenty of fluids when adding it into your lifestyle.

Luckily, adding ground flaxseed into your diet is super easy! There are many ways to enjoy it in recipes or as a topping. Flaxseed is naturally gluten free, but be sure to check the labeling for a gluten free statement and/or certification because of cross contamination.

Ways to include flaxseed in your diet:

  1. Make recipes like the Flaxseed Muffins below!
  2. Add a tablespoon of flaxseeds or ground flax to your favorite smoothie.
  3. Sprinkle ground flaxseed onto yogurt or your favorite cereal.
  4. Try adding 1-3 tablespoons of ground flaxseed to your favorite bread or muffin recipes. We love adding some to this Gluten Free Sandwich Bread recipe!

Flaxseed Muffins Recipe - soft, flavorful, and healthy! Everyone will love these flaxseed muffins. #flaxseedmuffins #flaxmuffins #muffins #glutenfreemuffins #breakfast

Can I add flaxseed to muffins?

Absolutely! Be aware that flaxseed absorbs a lot of liquid. This means you’ll only want to add a tablespoon or two of ground flaxseed to your recipe, or use a recipe such as the one below that is developed to include flaxseed without becoming dry and crumbly.

Why we love muffins…

We absolutely LOVE muffins at our house! Why??? First off, muffins are great for on-the-go eating, something our family needs more and more as time goes on! 

We love to keep muffins on hand for easy breakfasts, after school snacks, and any other time we need to grab something quick to eat on our way out the door. They are also super easy to make healthy and gluten free. 

Flaxseed Muffins Recipe - soft, flavorful, and healthy! Everyone will love these flaxseed muffins. #flaxseedmuffins #flaxmuffins #muffins #glutenfreemuffins #breakfast

Muffins are great for breakfast, school lunch, and more!

These flaxseed muffins are also great for school lunches because they have protein, fiber, healthy fats, and low-glycemic coconut sugar, meaning their blood sugar won’t spike and fall causing an afternoon slump. These muffins will keep your kids going and are a great way to start the day!

How to make flaxseed muffins:

Making flaxseed muffins is a cinch. They are quick, easy, and a crowd pleaser. Let’s go through the step-by-step instructions:

Real, healthy ingredients are all you'll need to make the most delicious flaxseed muffins. #healthymuffins #flaxmuffins #muffins #flax

First, gather your ingredients.

To make these muffins gluten free, you’ll want to be sure all your ingredients are labelled gluten free. Be aware that some brands of almond flour are packaged in the same facility as wheat products – always read labels and look for products that say “gluten free” and/or are certified gluten free.

Certified gluten free means the product tests at below 10 ppm of gluten, which is half the ppm allowed in products just labelled “gluten free”.

Learn how to make #glutenfree flaxseed muffins with easy, step-by-step instructrions.

Step 1:

Whisk eggs, then add remaining wet ingredients and whisk until smooth.

Flaxseed muffins are easy to make - we will show you how to make flaxseed muffins with step-by-step instructions.

Step 2:

Add dry ingredients and stir or whisk just until smooth. Almond flour is notorious for lumps, so whisk it separately before adding to your muffins to avoid lumps or over-mixing. 

As you can see in the photo, the muffin batter will be somewhat thick, but easy to scoop. If you notice that yours is too thick, add a tablespoon or 2 of milk. If it looks too thin, add a tablespoon or two of gluten free flour.

Flaxseed Muffins are so easy to make - delicious and healthy!

Step 3:

Divide the muffin batter between 12 muffin cups. we love using these parchment liners because no matter what kind of muffins we’re making, they never stick. We order several boxes at a time on Amazon so we never run out.

Bake until the muffins bounce back when you tap them, or until a toothpick inserted in the center comes out clean. Allow to cool for a few minutes, then serve!

How to store leftovers:

If you have leftovers, store them in an airtight container at room temp for a day, or freeze what you won’t eat in that amount of time. If you put leftovers in the fridge, they will get crumbly. We like to freeze them individually on a cookie sheet for 30 minutes to an hour, then put them all in a freezer bag. This will keep them from sticking to each other and make it easy to pull one out any time you want.

Looking for more healthy gluten free recipes? Here are a few of our favs:


Healthy Gluten Free Recipes


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Flaxseed Muffins Recipe - soft, flavorful, and healthy! Everyone will love these flaxseed muffins. #flaxseedmuffins #flaxmuffins #muffins #glutenfreemuffins #breakfast


Flaxseed muffins are a tasty way to add flaxseed into your diet! Packed with wholesome ingredients, flaxseed muffins are a recipe the whole family will enjoy. This recipe is gluten free, dairy free, vegetarian, and DELICIOUS.

Flaxseed Muffins (gluten free, dairy free, vegetarian)

Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 15 minutes
Total Time: 25 minutes

Finally, a healthy muffin that tastes great! These flax muffins are made with wholesome ingredients and are gluten free, dairy free, and easy to make.



  1. Preheat oven to 350 degrees.
  2. Line a muffin tin with liners (I absolutely love these parchment liners) or grease well. Set aside.
  3. Whisk eggs in a large bowl.
  4. Add milk, vanilla, sugars, and oil and whisk until smooth and combined.
  5. Add remaining ingredients and whisk just until all ingredients are combined.
  6. Divide batter evenly between twelve muffin cups using a large cookie scoop or a spoon.
  7. Bake muffins for 15-17 minutes, until a toothpick inserted in the center comes out clean. Cool and enjoy!
  8. You can store at room temperature for one day, or freeze for later.


  • We have tested this recipe with Better Batter and Grandpa's Kitchen flour. Both worked great, and your favorite flour should work as well.
  • If you don't have coconut sugar or cannot tolerate coconut, substitute brown sugar.

Nutrition Information:
Yield: 12 Serving Size: 1 muffin
Amount Per Serving: Calories: 200Total Fat: 12gSaturated Fat: 3gTrans Fat: 0gUnsaturated Fat: 9gCholesterol: 34mgSodium: 246mgCarbohydrates: 19gFiber: 2gSugar: 10gProtein: 4g

Did you make this recipe?

Please leave a comment on the blog or share a photo on Pinterest

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  • Reply
    Alisa Fleming
    March 18, 2019 at 10:45 am

    I absolutely love flaxseed! And I love that you didn’t use it as an egg replacer here, but as the star of the show instead. I’ll have to try these!

    • Reply
      March 18, 2019 at 2:16 pm

      Thanks Alisa, Hope you enjoy them! -Celeste

      • Reply
        Beverly J Day
        August 21, 2019 at 8:31 pm

        ok. 1) you need a “jump to recipe” button. 2) you need to cut the length of your recipes down so that they print on one page. 3) there is a mistake in your “Hatch Green Chili Biscuits”…it says “1/4 cold unsalted butter.” Does that mean 1/4 cup? Or “one quarter of a lb of butter?”

        • Reply
          August 23, 2019 at 10:16 am

          Hi Beverly, I appreciate the feedback. The reason I do not have a “jump to recipe” button is because I try to pack my posts with detailed info on how to make each gluten free recipe successfully. I would hate for you to waste your expensive gf ingredients! The same applies for the printable, if you would like to fit it on one page you are welcome to print on both sides of the paper or copy and paste, then reduce the font size to fit. I’ll head right over to the Green Chili Biscuits and fix that error, thanks for catching it! -Celeste

          • louise borg
            March 14, 2022 at 4:53 pm

            what does the “T” in ingredients under granulated sugar and baking powder mean? tsp or tbsp!!
            I baked these for an extra 3 mins as they were still a bit wet in the middle

          • thereislifeafterwheat@gmail.com
            March 18, 2022 at 1:58 pm

            T=Tablespoon, sorry for the confusion 🙂

  • Reply
    jenna urben
    March 18, 2019 at 2:06 pm

    Oh yum! These look incredible. I love using flaxseed. Will try these out very soon 🙂

  • Reply
    Jules Shepard
    March 19, 2019 at 12:43 pm

    Another fan of flaxseed right here and a true blue fan of muffins! These look so airy and delicious – looking forward to giving these a try.

  • Reply
    March 20, 2019 at 5:31 am

    I love muffins for breakfast! These ones turned out so moist, perfect recipe as you always deliver!

    • Reply
      March 21, 2019 at 10:59 am

      So glad you enjoyed them Noelle, thank you so much! -Celeste

  • Reply
    Sarah @ The Fit Cookie
    March 20, 2019 at 8:46 am

    Your flaxseed muffins look so light and fluffy! I bet they taste amazing, too 🙂

  • Reply
    Kristen Wood
    March 25, 2019 at 9:52 am

    I love how moist and fluffy these look!

  • Reply
    Carla Day
    March 31, 2019 at 4:19 pm

    I was wondering if these could be made with applesauce instead of oil and if that would reduce the amount of sugar needed?

    • Reply
      April 1, 2019 at 10:00 am

      Great ideas Carla! I haven’t tried either of these options, if you want give it a shot let me know how it goes! -Celeste

  • Reply
    Nicole Dawson
    April 9, 2019 at 8:41 am

    I love how light and fluffy these look Celeste! You’re the queen of GF breads

    • Reply
      April 9, 2019 at 9:46 am

      Thank you so much Nicole! -Celeste

  • Reply
    April 10, 2019 at 9:52 pm

    These muffins look so light and fluffy…I can’t wait to try them 🙂

  • Reply
    Erin Dee
    April 20, 2019 at 7:30 pm

    These look so delicious! Perfect for breakfast and snacks!

  • Reply
    April 24, 2019 at 11:11 am

    Can’t wait to try this muffin, I know my family will love it! If i don’t use vanilla, is it test well?

    • Reply
      April 29, 2019 at 6:27 am

      Vanilla definitely adds a beautiful flavor, but you can leave it out if you want. Enjoy!

  • Reply
    March 26, 2020 at 9:15 am

    Could I add cacao powder to these muffins? Would I need to add more liquid?

    • Reply
      March 26, 2020 at 9:45 pm

      I’ve never tried that, but it sure sounds like a great idea! I would decrease the flour by a bit and add a little baking soda. You may also need more sugar depending on how much cacao powder you add.

  • Reply
    May 3, 2020 at 10:11 am

    I have just started my gluten free (most grain free actually) journey and wow! These give me hope that it won’t be as bad (or hard) as I thought. These muffins are delicious, moist and satisfying. Thank you SO much!

    • Reply
      May 9, 2020 at 11:51 am

      So glad you’re enjoying the muffins Kristine!

  • Reply
    June 15, 2020 at 2:39 am

    I found your recipe and immediately put it to the test. I am on a no sugar diet so had to take out the sugar ingredients. I also skipped the gluten free flour for diet reasons given the carbs in the rice flour and just adjusted the amount of the flaxseed flour accordingly.
    Our 16 year old suggested blueberries and that was a great addition. I made a test muffin as a “one minute muffin” in the microwave, but preferred the texture of the batch I made in the regular oven. My wife loved them too, so they all went very fast, a big hit.
    We definitely need more wheat and grain free diet ideas.

    • Reply
      June 15, 2020 at 11:41 am

      So glad the recipe worked for you, thanks for sharing your subs!

    • Reply
      June 23, 2021 at 10:22 am

      HI Robert, might you explain what you substituted the sugar with. Did you remove both coconut and normal sugar? I was looking to remove the table sugar.
      thanks for inputs.

  • Reply
    August 23, 2020 at 8:57 am

    Is flaxseed flour same as ground flax seed? If not, can I use flaxseed flour instead?

    • Reply
      August 25, 2020 at 10:56 am

      Yes it’s the same thing 🙂

  • Reply
    December 6, 2020 at 6:04 am

    Do you have to use almond flour in order for these to turn out right? (nut allergies here). Thanks for sharing what you have learned…sure helps the rest of us

    • Reply
      December 7, 2020 at 10:24 am

      Hi Mary, You could probably sub cassava flour, I haven’t tried it in this recipe yet but I have with other recipes and I think it would work. Let me know! XO Celeste

  • Reply
    Mayen Ruiz
    December 16, 2020 at 7:09 pm

    Hi! This sounds like a great recipe as I’m looking for a neutral flavored muffin to make myself. I suffer from MANY food allergies, so I was wondering if instead of the almond flour, can I use the same amount of gluten free flour? Also, I’m allergic to egg so I will be using the equivalent in “flax eggs.” If it all works out this recipe will be loaded with flax meal which is not a bad thing! Thank you!

    • Reply
      December 18, 2020 at 8:46 pm

      You could try subbing cassava flour, but not a gluten free flour mix. I’m not sure on the flax eggs, if you try it please let me know how it goes!

  • Reply
    Mayen Ruiz
    December 18, 2020 at 5:11 pm

    Hello! I was wondering, instead of the almond flour, could I use the same amount of gluten free all purpose flour? I am allergic to almonds and don’t have access to other alternatives at the moment. Also instead of eggs can I do flax eggs? Also have an egg allergy. Thank you!

    • Reply
      December 18, 2020 at 8:43 pm

      Almond flour behaves very differently, you could try using cassava flour instead. I haven’t tried using flax eggs.

      • Reply
        Amy Menard
        September 3, 2021 at 3:06 pm

        Hi. I’m allergic to almonds but see in other comments you suggest cassava flour. I also have a oat/rice blend for my gluten free flour. Would this turn out okay? Do you think I would need to adjust to moist and add more oil or something?

        • Reply
          September 10, 2021 at 1:19 pm

          I haven’t tried something like that but you’re welcome to give it a go! I find this recipe to be fairly forgiving 🙂

  • Reply
    Rhonda Harris
    February 1, 2021 at 9:42 am

    These are absolutely delicious and so easy to make! I’ll be making these again…and again…and again!

  • Reply
    A. Roff
    April 11, 2021 at 2:25 pm

    Spectacular!! I made these about an hour ago, and just ate one. It took gobs of will-power to stop myself from eating a second one right away. Let me tell you about making them. My kitchen is tiny, and my baking items are in various places that I can fit them into. So it was a bit of a saga. I keep my almond flour in the freezer along with my flax meal, etc. I measured the almond flour and thought I’d closed the bag properly. NOT! Putting it back into the freezer, I saw almond flour trickling out of the bag onto other freezer items. Blue air ensued. Gangstas blushed. Then the same thing happened with the flax meal. Much unladylike language! But a very clean floor. Like another baker, Robert, I avoid sugar where I can, so I used 3 medjool dates and just a tablespoon of sugar. The dates were pulverized with the liquid ingredients, so no issues there. I used Bob’s 1 to 1 gluten free flour. I made only half the recipe because it’s just me and I don’t want to eat a dozen of anything. I added 2 raspberries to each muffin just before baking (genius idea, she said, humbly). Thank you for this highly successful recipe! By the way, for the people who can’t eat almonds, would they be able to sub something like pumpkin seed flour? Seeds are so full of oil that making a flour from them might be difficult, but it’s a thought .

  • Reply
    Heidi Lynn Borden
    August 19, 2021 at 7:15 pm

    I just made this recipe today and I must say I am soooooooooo pleased!! I have been looking for a flax muffin recipe that didn’t feel like I ate a brick afterwards. This recipe is truly wonderful!! I made some the way the recipe reads then I also made some with cocoa in them. The cocoa made them super yummy! I used canola oil in mine to keep them light and they certainly did not disappoint!! I ground my flax seeds and almonds fresh just before I made the recipe. I used 3/4 cup of brown sugar in place of the other sweetners. I really love this recipe! I am about to share it and keep it in my file of best recipes! I have subscribed to your page… I am looking forward to trying more of your recipes!! Thank you so much!!

    • Reply
      September 10, 2021 at 1:21 pm

      I haven’t tried adding cocoa, that’s a great idea! Thank you for sharing your review and adaptations. Happy baking! XO Celeste

  • Reply
    August 25, 2021 at 12:23 pm

    I make this recipe weekly (double the recipe=15 muffins). I must have eaten 1,000 of these muffins in the last year. They are delicious and healthy! The only muffins I make.

    • Reply
      September 10, 2021 at 1:20 pm

      So glad you like them! They’re my fav too 🙂

  • Reply
    March 3, 2022 at 10:25 am

    These flaxseed muffins look so delicious and wonderful. I just love these and must try this recipe. Thank you for sharing such a wonderful article and recipe.

  • Reply
    Lessley Dutton
    April 9, 2022 at 1:43 pm

    I would like to make these chocolate…how much cocoa powder should I add, and how much of any flour should I reduce in the recipe? Thx!!

    • Reply
      April 13, 2022 at 2:36 pm

      That’s a great idea! I haven’t tried it so I’m not sure, but please report back!

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