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Grain-Free Apple Flax Muffins Recipes

Apple flax muffins

We threw my sister-in-law a real curveball, coming to visit during Lent when our entire family was grain-free. I’m pretty sure she had a spectacular menu all planned out when I dropped the email bomb about, “By the way, we gave up grains for Lent, and it’s not just a sacrifice thing, but we have to stick to it to see if anyone actually has a health issue with gluten. Hope you weren’t planning veggie lasagna for a meatless Friday dinner…”

She was, of course. Then she was going to use eggplant in one dish instead of noodles, until I told her nobody around here likes eggplant, either.

The poor girl. I don’t blame her for being frustrated at first, and I felt horribly after speaking to her on the phone.

She never ceases to impress and amaze me, though, so I wasn’t completely surprised (although honored and touched) that she tossed her original plans and rose to the challenge with new recipes the whole weekend.

She learned to read labels, found some fun gluten-free crackers, served an amazing meat- AND grain-free supper on Friday (pasta-less minestrone, salad, and zucchini-based cheesy lasagna), and got creative with quinoa crepes for breakfast. (The only time my husband has ever eaten quinoa and enjoyed it! Woo hoo!) She found a little restaurant in Cincinnati for Saturday’s lunch that serves local, pastured meats and eggs which I raved about on Facebook as soon as I could, and she had bunless and delicious homemade turkey burgers with tons of side dishes for dinner.

I am so truly blessed to have a sister-in-law who cares about us so much. *sniff*

She even knocked out the ever-difficult “snacks” category with these apple flax muffins, a recipe she realized she had bookmarked long ago before she had ever heard of anyone going grain-free.

They were the absolutely perfect to-go treat for the 5K run/walk that we all participated in.

And now, for the recipe. You won’t trick anyone into thinking they’re not health food, but if you like a hearty muffin, you’ll never miss the flour in this recipe. I just love the chunkiness of the nuts and apples, and I remain amazed that flax can take the place of all grains like this.

You can even try swapping the sugar with sorghum syrup or maple syrup for a healthier sweetener.

Cover of Healthy Snacks to Go 2nd edition eBook
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Apple flax muffins
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Grain-Free Apple Flax Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.3 from 4 reviews
  • Author: Katie Kimball
  • Prep Time: 20 mins
  • Cook Time: 18 mins
  • Total Time: 38 mins
  • Yield: 1824 1x
  • Category: Breakfast


Units Scale

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  1. If using ground flax (meal):
  2. Mix dry ingredients. Beat the eggs and add to dry mixture along with oil, applesauce, and vanilla. Mix thoroughly. Add apple and nuts and stir to combine.
  3. If using whole flax seeds; you’ll need a decent blender for this one:
  4. Blend eggs, oil, flax seeds, applesauce and vanilla about a minute, or as long as it takes to grind up the seeds completely. (This just about killed my blender, so I decided “good enough” when my blender just didn’t want to move anymore.) The mixture will get very gummy and thick quite quickly.
  5. Combine dry ingredients separately.
  6. If you have a high-powered blender, add dry ingredients to the mixture in the blender and blend to combine, then stir in apples and walnuts.
  7. If you have a regular blender, pour wet mixture from blender into a bowl, where you can combine with dry ingredients, apples and nuts.
  8. To finish either method:
  9. Allow fully incorporated mixture to stand 10 minutes.
  10. Preheat oven to 350 degrees F. Line or grease muffin tins. Spoon into tins (the batter will be very thick) and bake for 18 minutes or until a toothpick inserted in the center comes out clean. (12-14 for mini muffins)

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I recommend storing any baked good made with flax in the refrigerator, unless you’re going to consume them all within 1-2 days. Flax just seems to mold quickly, possibly because of the unstable omega-3s that are so healthy for us to eat. (More on how to store flax seeds and flax oil.)

I also recommend, of course, enlisting the kids to help on this one like the pic below! Yes, kids CAN use sharp knives safely on those apples, measure ingredients carefully and stir a uniform mixture…we teach them how in our online kids cooking class, in fact. 😉

Apple flax muffins

Like I told you last week when I detailed the difficulties of our elimination diet, eating with others is the greatest challenge. I’m so thankful my sister-in-law made it really, really easy on us for an entire Lenten weekend.

If you’re just here for the healthy snacks, you might also enjoy these banana flax muffins (although not grain-free), found in my Healthy Snacks to Go eBook.


I’m thrilled to share a FREE gluten-free cheat sheet mini eBook to help get you started! This is perfect if you’ve just been told you need a GF diet, if you have a friend or family member eating GF and you’d like to cook for them, or if you’re just curious what it’s all about!
Apple flax muffins

See my full disclosure statement here.

Unless otherwise credited, photos are owned by the author or used with a license from Canva or Deposit Photos.

53 thoughts on “Grain-Free Apple Flax Muffins Recipes”

  1. These are awesome thanks! I added more than 1 apple, and my batter was dry so I added more applesauce.

  2. I use a small amount of minimally refined organic cane sugar or organic Maple syrup! Yum! I also throw in organic oats, GF flour and Flaxseed, yum! I use my granny smith apples which I love, I first chop them into small pieces and nuke them till a little soft, Yum!

    I love baking but seldom if ever can adopt an online recipe. They are always either tooo fancy with their ingredients or tooo poisonous AKA unhealthful.

    Sincerely and Thanks for Recipe,
    (retired baby-boomer)

  3. Wow! Thanks for the base recipe. I used maple syrup instead of sugar and I didn’t have an apple or walnuts so I added 1 cup of ricklands organic trail mix (pumpkin seed, sunflower seed apple, cranberries, almond). It’s very light and puffed up really nicely and holds together really well. I usually bake with almond and coconut flours. Thanks again!

    1. Hi Elizabeth,

      Coconut butter is basically like a nut butter so it isn’t the same as oil. It contains actual coconut, ground finely, and also coconut oil. I’d definitely use coconut oil or you could sub in butter.

  4. Hey Katie. Love these muffins! Wondering if other fruit would work instead of the apples for some variation? Think these will be staples around here! Ever tried another fruit or think it would work? My son wants me to try strawberry or peach. I buy these bulk in season and freeze and didn’t know if frozen fruit would add too much liquid to the recipe?

    1. Katie Kimball @ Kitchen Stewardship

      Oh, dear, I’m so sorry you had a bad experience with the muffins. Did you change anything about the recipe? Was your ground flax perchance a little old, or stored at room temp? Flax is very delicate and goes rancid quickly. What is inedible about the muffins, if you can describe it?
      Thanks for helping me troubleshoot the recipe (you’re the first to have a problem with it) – Katie

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  6. Do you have the nutritional info on these somewhere on your website? I made them last night and they are so good!! I want to eat them all the time now 🙂 I didn’t have quite enought flax so I filled the last 1/4 cup with chia seeds and it came out great.

    1. Katie Kimball @ Kitchen Stewardship

      Awesome to know about the chia! I don’t have calorie counts on this recipe, but when I do it, I just plug it into here:

      Easy as pie…er, muffins! 😉 Katie

  7. I just made these and have never made anything grain free before. So this may seem like a dumb question but are these super, super moist? I did everything the same as the recipe but instead of applesauce I used some homemade apple butter. My toothpick came out clean and they are delicious but I am wondering if they are under cooked(even though I cooked for 22 mins). Should they be exactly like a muffin in texture?

    1. Katie Kimball @ Kitchen Stewardship

      Not a dumb Q at all – they ARE very moist, and many grain-free recipes are similar. I’m hoping you enjoyed them thoroughly, since it’s a week later when I saw the comment here1 😉 Katie

    1. Try this it works well with Chia Gel

  8. thanks! I actually made them and gave her about 1/4 of a muffin (she loved it by the way!) So far so good… I’ll let you know if anything changes 🙂

  9. Minus the honey do you think these would be ok for a 10 month old? I’ve been trying to do research about whether or not whole eggs in baked goods are a problem before age 1 but I have found mixed info. Thanks!

    1. Katie @ Kitchen Stewardship

      My little guy is 10 months right now, too, so I’m asking the same question. Whole eggs in baking aren’t any different than scrambled eggs, so you have to answer the “will we do egg whites” question at all. Other than that, staying away from grains is a good idea for under 1yo, but I’m not sure about this much flax, I guess…for some, it can affect digestion…hmmmm…not much help, am I? 😉 Katie

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  11. We used egg replacer (I believe the brand is EnerG) and it didn’t turn out. I also used agave instead of sugar or honey… 30 minutes in the oven and they were till gooey in the middle. 🙁

    @Mary Jo, I hope the elimination diet works for your husband! My husband tried gluten free and it didn’t help, then got a blood test done and tested positive for 28 different food intolerance’s. It has now been 7 weeks and he is off of his Asthma and allergy medicine for the first time in his adult life. (and has been since week 1 of the elimination diet!) He’s a new man, it’s amazing. Anyway, all that to say, good luck!

  12. Mary Jo @ Covenant Homemaking

    Do you think subbing flax meal & water for the eggs would work in this recipe? We’re about to start en elimination diet for my husband to see if we can figure out the cause behind his asthma, so for the first two weeks (and maybe longer?) there’s no wheat, eggs, soy (which is fine–we don’t eat it anyway), corn, peanuts, or dairy.

    1. Mary Jo,
      It should, as far as I know…let me know how it goes, I love being able to answer for sure for others! 🙂 Katie

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  15. via Facebook

    My daughter has a rare food allergy (she has an anaphalactic reaction to) flax. I might give these a try myself, but do you know of any substitution?

    1. Kimberley Hensen

      You could try chia seeds instead of the flaxseeds and see if that works.

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  18. Made these yesterday and they’re already nearly gone. Very yummy! I didn’t have quite enough flax meal on hand, so I used 3/4c flax meal and 1/4c coconut flour (left the rest of the recipe the same) and they still turned out. Thanks!

    And I second the request for the quinoa crepes!

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  20. I have a recipe very similar to this and it doesn’t have any applesauce. It is almost exactly like yours but calls for 1/2 cup water instead of the applesauce. I have made them and really like them but I do think they would be better with applesauce. Are we going to get the recipe for the quinoa crepes? They sound really good!

    1. Co,
      Good question – I may have to beg my SIL for the crepes recipe, as I didn’t get that one yet. 🙂 Katie

  21. These sound so yummy! Thanks for sharing the recipe!

    I usually grind flax seeds in my coffee grinder. It might take a couple of rounds to make enough, but I’ll probably try grinding them all first. I’ve already burned up two blender motors, so I’d rather not do that again! 🙂

  22. Yummy. I just made them, not b/c we’re gluten free but I’m trying to eat less grains for weight purposes. I had some butternut squash puree but no applesauce, so I used that. My vitamix kept overheating though. Next time I’ll process the flax seeds dry b/f adding the wet stuff.

    1. Allison,
      Great idea for a substitute! If your Vitamix was overheating, I don’t feel so badly that I thought I was going to kill my blender… 😉 Katie

  23. How absolutely wonderful that your SIL went the extra mile to cook grain free for you all. We’re lucky to get any food that didn’t come out of a box or from a delivery car when we visit ours, lol. These look great!

  24. I am SOOOOOO making these tonight. I’ve been waiting for them for what seems like FOREVER! 🙂

  25. Adrienne @ Whole New Mom

    I was just going to ask the same question that Jennifer did. Just a warning, I tried the fat for applesauce sub recently for cookies and they turned out just passable in a huge sea of melted fat. Ugh! Any other ideas?

    I am having to not eat fruits for awhile so hmmmm…maybe the yogurt is a good idea and sometimes if I make homemade coconut milk or rice milk and make it thick that can do the trick as well. Thanks for the ideas, Katie!

    I love flax too. I have a nice focaccia flax bread recipe on my site that I think you would love. I took it to our church’s small group and they downed it :-)!

  26. These look good! Have you checked with traditional foods folk to see if flax seeds are negatively affected by cooking? I feel like I’ve heard that somewhere, but can’t remember…

    Also, I made the grain free granola that you recommended and made a couple changes. I did 5 cups of various nuts and seeds and then 5 cups of the big coconut flakes. Much less dense and crazy-crunchy. The coconut flakes have a great texture after they’re cooked and make it seem like a normal granola! Just thought I’d throw that your way…

    Thanks again for all the ideas!

    1. Melanie,
      On that flax storage post I link to above, I have a source in the comments about baking with flax- basically, it doesn’t actually get up to temps high enough to be a problem.

      Great idea on the granola! My grandma tried it and asked for the recipe, then said “no way” 10 minutes later when she was still chewing and picking stuff out of her dentures!!! the coconut might help… 😉 Katie

  27. This looks yummy!!! I want to make today but I dont have applesauce…is there anything else I can use?

    1. Jennifer,
      Seems like applesauce is often subbed in for a fat, so maybe another 1/2 cup of melted coconut oil or butter would work! 😉 You could also blend up some apples, raw, to make 1/2 cup or even try yogurt. Now we’re getting experimental – if you try any of those, please come on back and let us know if it’s a workable variation and I’ll update the post for others. Thanks and good luck! 🙂 Katie

      1. I’ll let you know how they turn out for sure. I’ve got the batter sitting right now. I used yogurt cause that’s what I had, I only had two apples and one was claimed for snack. Right now the batter looks yummy!

      2. They came out great. We’re new to gluten free and my girls are begging me fore another. The texture is one I have to get used to, I’m not used to flax meal but I like it. The taste is wonderful and we love nutmeg and it comes through nicely. They were moist but not soggy and rose nicely considering I used baking soda instead of powder, since that is all that I had as well. I would rate this recipe five starts easy, if there was a rating system 🙂

        Thank for sharing, this one is a keeper for sure!

      3. What about using avocado instead of applesauce? Or does it not do well in heat? Just popped into my head when I loved in the fridge a noticed an avocado that needs to get used…it’s a fat right? Why couldn’t it be subbed as a fat? Have you seen it done?

    2. We are doing a similar “test” in our household for gluten sensitivity, but our children (collectively) have severe allergies to eggs, dairy, nuts and my daughter is anaphalactic when she has flax (a rare, but very serious food allergy that was diagnosed after ending up in ICU). These sound so good, though, I might try a batch for myself!

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