Flax Carrot Apple Muffin Recipe

Have you ever started to make school lunches in the morning to find out you were out of bread?  This happens to me like once a week, at least! On these days, I try to send these Flax Carrot muffins in their lunch instead of a sandwich!

Flax Carrot Apple Muffins. Check out the 10 AMAZING benefits of flax!


I can’t believe I haven’t shared this Flax Carrot Apple Muffin Recipe yet! It’s one of my kids favorites, and I’ve been baking them for years.  Although the first few times they actually Did NOT like them (just a warning).  The original recipe is posted on Bob’s Red Mill package of Flax meal, but I’ve changed it a bit to pacify my children’s tastes.

Why Flax? Tosca Reno’s book, The Eat- Clean Diet for Family and Kids has an entire chapter on pooping!  Flax helps the constipated child POOP!  We all want that for our kids, right?  She says Flax seeds can:

  1. Help build lean muscle tissue
  2. Promote regular, healthy elimination
  3. Stimulate lazy bowels
  4. prevent blood clots from forming
  5. reduce high blood pressure
  6. promote weight loss
  7. increase energy levels
  8. increase metabolism
  9. promote optimal organ function- brain, nervous system, skin, sexual organs
  10. Provide energy

Convinced yet?  Make these flax muffins for a powerful way for your kids to start their day!

Flax Carrot Apple Muffins

  • 1 1/2 cup whole wheat flour (I actually used white, but the original recipe calls for whole wheat.)
  • 3/4 cup Flaxseed meal
  • 3/4 cup oat flour (by grinding oats in blender)
  • 1/2 cup brown sugar
  • 2 tsp baking soda
  • 1 tsp baking powder
  • 2 tsp cinnamon
  • 2 cups pureed or shredded carrots  (the first few times I pureed so the kids wouldn’t notice the carrots)
  • 2 cups shredded apple
Flax Carrot Apple Muffins. Check out the 10 AMAZING benefits of flax! Flax Carrot Apple Muffins. Check out the 10 AMAZING benefits of flax! Flax Carrot Apple Muffins. Check out the 10 AMAZING benefits of flax!

In separate bowl

  • 3/4 cup milk
  • 2 eggs
  • 1 tsp vanilla
Flax Carrot Apple Muffins. Check out the 10 AMAZING benefits of flax!

Combine dried ingredients with the wet. Add

  • 1 cup dried cranberries
Flax Carrot Apple Muffins. Check out the 10 AMAZING benefits of flax!

Combined just until moistened. Fill muffin papers. Bake at 350 for 10 minutes (mini muffins) or 15 minutes, large muffins.

I love having hearty muffins like this on hand for my kids. They are appropriate for all meals: Breakfast, lunch, snacks, etc.

Other ways to use flax

Flax Carrot Apple Muffins. Check out the 10 AMAZING benefits of flax! My kids have spring break this week…My husband agreed to a week’s worth of grave yard shifts.  That means all week I’m trying to keep kids quiet, not letting their friends in the house.  It’s too yucky to play outside.  And Wade is trying to sleep through it all.  What a bad week for graveyards!

Flax Carrot Apple Muffin Recipe

Flax Carrot Apple Muffin

Flax Carrot Apple Muffin Recipe
Serves: 12
Cook Time: 10 m


  • 1 1/2 cup – flour, whole wheat
  • 3/4 cup – flaxseed, ground
  • 3/4 cup – oats, dry
  • 1/2 cup – brown sugar
  • 2 teaspoon – baking soda
  • 1 teaspoon – baking powder
  • 2 teaspoon – cinnamon
  • 2 cup grated – carrot
  • 2 cup, grated – apple
  • 3/4 cup – milk
  • 2 large – egg
  • 1 teaspoon – vanilla extract
  • 1 cup – cranberries, dried


  1. Make oat flour by grinding oats in blender. Grate or puree carrots (will need two cups.) Grate apples.
  2. Combine dry ingredients.
  3. In a separate bowl, mix milk, eggs, vanilla.  Add to dry ingredients just until moistened.
  4. Stir in cranberries.
  5. Fill muffin papers.
  6. Bake at 350 for 10 minutes (mini muffins) or 15 minutes, large muffins.

Nutrition Facts

  • Nutrition per serving % daily value
  • Calories: 211 11%
  • Fat: 6 g 9%
  • Carb: 34 g 11%
  • Fiber: 6 g 24%
  • Protein: 6 g 12%
  • Sugar: 14 g
written by
Amy Roskelley

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Don Johnson says:

Made them exactly to the recipe
they were not cooked at 15 min &
they stuck to the paper cups in the pan
Other wise very good

Isha McCarthy says:

Hello! These look delicious and sounds very easy! I just have a couple of questions:
– I only have all purpose flour, is that okay?
– We JUST ran out of oats- if I omit that what modifications (if any) need to be made?


Natalie Monson says:

Yes all purpose flour is ok in these muffins. Also, you can just omit the oats and use more flour. We haven’t tried it that way, but it should turn out ok. Good luck!

Elle says:

My only complaint is the enormous prep work that went into this (grinding oats to create oat flour, grinding flax seeds to create the flax meal, grating carrots, apples). I didn’t modify the recipe much, but used more grated apple and oat flour because I didn’t want to throw the rest bits out. Unfortunately, I only had sweetened dried cranberries, so next time I’ll use less sugar. Family loved them. BTW, I live in Europe and we don’t bake using volume, but weight, so I just used what I thought was a cup and went from there.

Stacy says:

Hi Amy! Have you tried making these with gluten-free flour, or a flax egg yet? Or both? 🙂 Just wondered how they turned out before I attempted it.

Devlin says:

I followed the recipe very closely. It makes around 16 standard-sized muffins. The bake time should be closer to 20 minutes and adding a little salt (1/2 tsp) would improve the flavor significantly. I like how healthy they are but they will be hard to finish as-is, undercooked and lacking in flavor.

Oralea Howard says:

Made these today with my 6 year old… after some initial nervousness, they came out pretty tasty! After baking for 10 minutes they were still pretty squishy so I cooked them for about 5 minutes longer than suggested, until the top had a bit of firmness to it. We made the mini muffins and used the ingredients as suggested except the cranberries… substitute mini chocolate chips. 🙂 These will be a great after school snack.

DAWN says:

I am assuming the oats are Old Fashioned Rolled Oats.

Has anyone tried this with Steel Cut Oats?


Jackie says:

Dawn, I do not think you can use steel cut. Old Fashioned are flattened out and absorb liquid much easier. Although I have yet to try this, you could experiment and cook some steel cut oats so that they close to be fully cooked but more firm. Then, add them to the recipe. Basically, use less liquid when cooking the oats since there are other ingredients within the muffins that make them moist. Oh, yes, and cut the recipe in half so that you are not wasting too much of the ingredients if they don’t come out right. Let me know how it goes!

Jenny says:

Thank you for sharing this wonderful recipe! I made these today and they turned out delicious!

lizzy says:

What should I use for an egg substitute? Usually, I use flax meal but this is apart of the recipe?

Paul Pedraza says:

This recipe looks good. Can the flax be substituted with another dry ingredient such as more flour? Or would you have any suggestions for a substitute? Looking forward to making these!

Karen says:

Hi, may I know how long can I keep these muffins in the fridge? Frozen?? And how do I actually heat them up before consuming? If I use oven to “bake” to heat up, will it get burnt? I tried using microwave to heat up but it became rock hard

Melinda says:

Hi! Making these for my daughters class… Didn’t see how many does this recipe make? Need 30? Thanks!

This makes 12. Double your recipe!

Enza says:

12 regular sized muffins?

Candlle says:

Could I use rolled outs instead of the oat flour, and flax seeds instead of milled flax.

I haven’t tried those substitutions Candlle, but let us know if you do!

Anne says:

Was so excited to try these 🙁 unfortunately they have been in the oven OVER AN HOUR and still wet in the middle? I followed the ingredients to the T. What could have happened? :/

Oh no Anne! that doesn’t seem right. Was your flax in “meal” form, ground up?

Anne says:

It simply says ‘flax seed chia blend ready to eat’ it is ground. Perhaps this kind doesn’t work. I’m attempting avian as we speak!

Marie Nicole says:

Do you happen to know the calories in this muffin? I’m so looking forward to trying these! I think I found a similar recipe a while back, bought all the ingredients but haven’t made them yet. I’m so glad I came across this recipe!

Erin says:

Should I use Red or Green apples?

Either one is fine Erin!

Sophie says:

How can I make this egg free pls? 🙂
My little girl is alergic..

sophie! I actually just found out I was allergic to eggs as well! our best substitute is a flax/water mixture. The details are here: https://www.superhealthykids.com/the-essential-food-allergy-substitution-guide/

Sophie says:

Thank you Amy! I used to use flex eggs too before, I was just wondering how to do with this since there is flax meal in it already.. add more which I mix with water or maybe mix it with the milk and let it stand for a while!? Oh well, I will try and let you know!
Did you become alergic to eggs as a grown up Amy?
Mayas allergy might be my fault, I was eating sooooo much eggs when I was pregnant with her and also when breastfeeding. She had eczema and I didn´t know what caused it until I gave her eggs for the first time. Now she is close to 4, didn´t get eggs since than and hope she grows out of it.. it would make things easier. Now when I make panncakes I make regular with eggs for my little boy as he loves them, egg free for her and carb-free for my hubby who is on LCHF diet. Crazy lol..
We love your website and recipes, I hang out here often! 🙂

Tim says:

I just made these. I have twin 17 months old kids so i don’t have much spare time but I wanted to make these for them because the ingredients are so nutritious. What a waste of my precious time. I’m throwing them away they are that bad. Honestly do not make these you will regret it. Horrible!

That’s a bummer Tim. This is actually a recipe right from Bob’s Red Mill package and is actually quite popular with most people. We love it here.

Danica says:

I have one of the pickiest 3 year olds you will ever come across (and also have 11 month old twins so not much free time to spare either) and she is devouring one as we speak…if that’s not a stamp of approval I don’t know what is! My husband and I liked them too! Wasn’t a waste of my time at all 🙂

More to the point, it wwas an ongoing franchise around which profit (I know that’s a dirty wor
to some of you. Should you truly need parts 10 or even 20 years in thhe future,they are accessible from the brand.
When the bowels aare rgularly moved and cleansed, the ennd result shows in radiant and a more youthful glow of the skin.

Amy says:

@Jamie! Thanks for letting us know- we love this one too.

Jamie Witkowski says:

I made these this past weekend for my 1 year old. I ended up pureeing the carrots and apples (great idea). He loves them! I made some bigger ones for me and my husband and we love them too! What a great, easy recipe to sneak in some fruit and especially veggies. Definitely making these again!!!

Amy says:

There is almost no flavor to this Debra!

Debra Pearson says:

What does flaxseed taste like?

Gail says:

I have substituted oat flour-the texture is a little bit different but it worked it well for us!

Amy says:

I bet it would be fine Leeanne, although I haven’t tried it myself. If you do it, let us know how it turns out!

Leeanne says:

I cannot have wheat .. Can I subsitute all
Oat flour for the whole wheat flour??

Amy says:

LOL!! Oh dear! And you still eat them?? Ha ha!!

Gail says:

These have become a staple in our house! Everyone *loves* them. My sister in law has dubbed them “Poo Muffins”!!

Amy says:

Thanks for your tips Katie!
For 12 muffins, it’s around 230 calories per muffin! Kind of high, but they are good calories, right? Lol.
So, if you made 15 of them, it would be closer to 184 calories per muffin.

Katie says:

Oh, also… I use whole oats for the oatflour and actually sub the wheat flour for oatflour instead. You must add 2.5 tsp baking powder to the recipe though… LOVE this muffin. Its my
Go-to breakfast, for me and my son!

Katie says:

How many calories if we make a batch of 15? I love this recipe, by the way. Ive been mAking a batch a week for about 2 months now.

Yolande says:

I just made these, but made several changes: I added earth balance butter, replaced milk with almond milk(we’re lactose intolerant), and replaced oatmeal with coconut flour. It loved and so did my 1yr-old daughter. Thank you for posting this.

Next time, though, I’ll add more milk, some nutmeg, and maybe some honey because they needed something extra and were a bit dry.

Amy says:

I can’t wait to try these! I put flax meal in a lot of items – even my no-bake cookies! – and love it. I have it mixed in my breakfast yogurt most mornings. I lost a recipe for flax carrot apple muffins I used to use and this looks the same without the protein powder. This will be perfect for my stepdaughter to take to school for her snack since her school lunch isn’t until 1:40!

Lou says:

Ok I take it back DS aged 5 just grabbed one ate it and rubbed his stomach making some weird MMmmmm noise! I almost fell over 🙂

Lou says:

I just made these I think I will puree the apple and carrot next time, I haven’t tried it out on the kids yet but to me the texture is off with the amount of grated ‘bits’ in it, the taste is nice though so definately a keeper with some tweaks for my liking!

Brittany says:

Loved! Used low fat buttermilk instead of low fat milk. Very very Yummy and warming.

Carrot and apple is very good comination to cook healthy muffins. I will try it

[…] yesterday, I’m anxious to have portable food I can take with me this weekend. I found this recipe from Eat Clean for Families and Kids and decided to give it a […]

Julie Gosselin says:

I was so excited about this recipe – my kids LOVE apples and carrots. I made these muffins today and gave one to my daughter for snack after school. In return she gave me a “I don’t really like these”. Grrr. When I questioned her she said “If it was just plain I would like it.” She did not want the apples visible – i.e. I should have pureed them.

I am struggling to find things my kids will eat that isn’t processed JUNK!

I saw the warning about your kids not liking them the first time. I may just freeze these and try them in a day or two.

Marisa says:

I’ve made these muffins several times so far this school year and never the same way. lol Tonight I made them with shredded zucchini and unsweetened applesauce. I’ve also made them with pureed pumpkin and applesauce. I made them the first time and felt they were a little bit bland (I was afraid my kids wouldn’t like them)….added just a little splenda in addition to the brown sugar the last two times and found that a cinnamon blend (cinnamon, nutmeg, allspice, orange peel) that I bought at a home cookware party gave it just enough “something” to make all the difference with my two little ones and my husband. Thank you for this wonderful recipe….I have enjoyed coming up with alternate recipes based on things my family likes, and to keep them from getting bored. Next we will try adding a little banana (and if that doesn’t work, I’ll add banana extract to the original recipe.)..it’s also fun adding things like walnuts and regular raisins. I’m just so happy my family loves these as I am working hard to introduce healthier snacks for school and home. This is a keeper, and I’ve referred several other Mom’s to this site. THANK YOU!!

Pao says:

Great ideas for flavor combos!

Kristen says:

I just made these tonight and LOVED them! My husband even said they were good which is HUGE! 🙂

I used 1 cup all-purpose flour (slowly working on switching to whole wheat) and 1/2 cup whole wheat. I also didn’t make oat flour just left the oats whole which I think gave them a nice texture. I discovered that when shredding apples you need to use the coarse side of the shredder or you make apple sauce. 🙂 And I put the apple peels and half of the carrots in the blendtec and pulverized them into a liquid.

According to the about.com recipe analyzer (I got 16 big muffins) they have 151 calories, 3.8g of fiber, and 47% of your daily of Vitamin A!

Great recipe, I’m excited to try others!

kendra says:

update! they turned out great! even my super-picky 6 year old had one and said he liked it. Everyone (6, 5, 3 & 1) ate them. It’s rare we can find something that pleases everyone…We will be making them again!

Amy says:

The pressure is on for my recipe skills! I’m a little nervous. I really, really hope you like them!!

kendra says:

mine are in the oven as i type. I processed the heck out of the carrots and apples (so they were more a puree-consistency…did it in the vita mix and added the milk during this step to keep things smooth) as a few of my boys will freak out if they see anything resembling a carrot or apple. I also omitted the craisins for the same reason. they smell good…can’t wait to try them!

Amy says:

Thanks for the feedback Lynn. Some healthy things I just have to get used to also! Definitely not a Coscto Pumpkin muffin 🙂

Lynn says:

I made these this weekend to take to our ballgames. The kids loved them. For me they were “different.” I’m not used to the flax tatse I guess, and they are not sweet. But after having several mini ones they grew on me! 🙂 Other mom’s at the ball field loved them too!

Amy says:

Hi Tina,
I do buy it ground and keep it in the fridge. I feel like we use it fast enough that it doesn’t go bad. Interestingly though, the ground flax meal they sell at Costco claims that due to the low temperature they grind the flax, that it lasts up to a year?!? I haven’t looked into it to see if that is true or not, but that is what the package claims.

flax meal – do you keep it in the freezer? Doesn’t it go bad pretty fast if you already have it ground? (I’d never take the time to grind it myself)

Liz – I would think you could substitute applesauce. Apples are going to have a lot of moisture and applesauce shouldn’t have more – maybe a little less? Apples though are going to give you fiber & all the whole vitamins and minerals.

Amy says:

Liz- I’m not sure, if I try it, I’ll let you know!

Amy says:

I did already cut back on the brown sugar, but I’m sure you could even more.

Liz says:

Do you think I could substitute applesauce for the shredded apple or would that throw off the moisture?

Susan says:

Golden is supposed to be higher in whatever it is that’s good, but brown works just fine. Golden is a little pricier, too. Love the recipe. I’m anxious to try it. Can I cut down on the brown sugar? Should I used something else to sweeten it like applesauce?

Amy says:

Stacey-still working on the golden flax thing. Not sure.. anyone know?

Amy says:

Yes, they are the same.

Liz says:

I think I’ll try to get my mom to make these while she is here. It’s so annoying to find new recipes I want to try and not be able to make them! Is flax seed meal the same thing as ground flax seeds?

Amy says:

Normally, yes- wheat flour! These, this morning, no. I’m out and had to return my Mother in law’s wheat grinder to her!! But it works perfectly fine!

Jessica says:

hehe – love your reasons to get us to eat more flax!!
And great recipe. I’ll have to peep the other suggested ones, too! Did you make these with whole wheat flour?

Amy says:

I used a cheese grater. I used the food processor to blend up the already shredded carrots a little bit. My food processor is really small, but it was only $25 at Costco, and it’s been GREAT!! I would love a big one though.

laura says:

looks like a great recipe! so, this is a very basic question, do you shred your carrots and apples in a food processor or with a peeler? (or a julienne slicer?) I don’t have a food processor but am thinking of investing in a good one.

Traci says:

I know what you mean. I just posted on this today too. Hope it warms up soon, but glad we’re spending the weekend in St. George. Hang in there! I know it’s hard. Oooo. Maybe we can get the kids together for lunch this week and I can finally meet you!

cathy says:

These sound yummy! I put flax meal in practically all of my baked goods. In addition to all of the lovely benefits you listed, it’s a little omega-3 boost!

Oh my word! These sounds amazing! I just emptied my bag of flax meal. I love Bob’s Red Mill. My mom once gave me a bag of golden flax seed. Do you know if there is a difference?
I’m so thankful for your blog. It’s great to have the support and inspiration of someone so health conscious. Thanks!

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Join over 100k + subscribers and get family-friendly recipes, picky-eater strategies, lunch-packing tips and more, delivered each week to your inbox.