Want healthy meals your kids will love?

Flax Carrot Apple Muffin Recipe


Your next picky eater success is here! Flax Carrot Apple Muffins load up kids on nutritious ingredients like whole grains (two of ’em!), fruits, veggies and seeds. Make these muffins ahead for a quick weekday morning breakfast or school-safe packed lunch option.

healthy whole grain flax muffins

Classic muffins like blueberry are fabulous. But isn’t it fun to have something a little surprising in your recipe box?

Here’s a muffin to spice up your repertoire that’s bursting with apples, carrots, cranberries, and the goodness of whole oats and flax seeds. It’s a moist, wholesome muffin that still appeals to kids who might be short on their daily servings fruits and veggies.

Five Reasons to Love This Recipe

  1. There’s SO much nutritional variety in these tasty muffins, they can serve as a complete meal. We pack in fruits, veggies, two different whole grains, AND flax seeds for a balanced, nutritious muffin.
  2. Picky eaters love them. If you’re struggling to get healthy ingredients into your kids, this recipe is nearly a sure bet. Nothing is quite so approachable as a delicious muffin.
  3. You can bring them with you. Hand one to your kiddo on your way to school. Pack them in lunchboxes. Bring them to the park. These muffins are a clean, handheld snack.
  4. You can freeze them. Double the batch and put some in the freezer for quick breakfasts or snacks down the line.
  5. They taste hearty, delicious, and sweet. Enough said. 😉
carrot apple flax muffins in a stack

Humble Flax is Super Good for Kids

Flax seeds are rich in nutrients kids’ bodies need to thrive. One tablespoon contains around 2 grams of fiber and almost 1,600mg of omega-3 fatty acids.

Omega-3-fatty acids, famously found in fish, benefit heart health by lowering cholesterol and reducing inflammation in the arteries. We might not be thinking about our kids’ cardiovascular health when they’re small, but teaching them to love flax now can have lifelong benefits.

The fiber in flax can help regulate digestion and help kids stay satiated after a meal. (That means they’re less likely to come begging for another snack 30 minutes after eating. Always welcome!)

These muffins don’t pay lip service to flax seeds: there’s 3/4 a cup in this recipe! That’s more flax seeds than sugar. So you can feel confident you’re packing in the nutrition.

close up healthy muffins with carrots and cranberries

Why Use Ground Flax Seeds? (+ Two Ways to Grind it Yourself)

You’ll want to use ground flax seeds in this recipe for two reasons. First, grinding the flax helps these mighty little seeds incorporate with the flour for a smoother, picky-eater-friendly texture.

Second, grinding the flax seeds releases the beneficial omega-3 fatty acids from the tough shell. This lets our bodies better absorb the nutrients in flax. (In general, using whole flax seeds in a recipe adds a nutty crunch, but our digestive tracks can’t easily break them down. Left un-ground, they can pass right through us intact. If you know what I mean.)

If you only have whole flax on hand, you can easily grind it right in your kitchen.

One way to do this is to toss your flax seeds into a high-speed blender and buzz them up. (You can even do this before you add the oats. Then add the oats right on top of the flax meal. Boom! Now they’re mixed together.)

You can also grind flax in a spice or coffee grinder, though be aware you can sometimes pick up the flavors of spices or coffee this way.

apple muffins with shredded carrots and seeds

Tips for Making and Storing Flax Carrot Apple Muffins

This recipe is simple to make because it follows the basic principals of muffin-making made famous by almost all muffins everywhere.

What that means is: mix up your dry ingredients in one bowl. Mix your wet ingredients in another. Gently fold them together, then voila. You’re ready to spoon them into a muffin pan and bake.

If you love to save yourself dish duty, feel free to use your blender cup as the “bowl” to mix your dry ingredients together. You’re already using it to grind your oats into flour, and maybe also your flax seeds (see above.) Just dump the grains, sugar, and leaveners into the blender cup and pulse a few times to mix.

When these muffins are cooked and cooled, you can toss some in a zip-top bag and store them in the freezer. Move frozen muffins from the freezer tot he fridge the night before you plan to eat them, so they’re defrosted by morning.

More Recipes Featuring Flax

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3.8 from 243 votes

Flax Carrot Apple Muffin

Your next picky eater success is here! Flax Carrot Apple Muffins load up kids on nutritious ingredients like whole grains (two of ’em!), fruits, veggies and seeds. Make these muffins ahead for a quick weekday morning breakfast or school-safe packed lunch option.
Cook Time15 minutes
Total Time15 minutes
Course: Breakfast
Cuisine: American
Servings: 12
Calories: 211kcal



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



Calories: 211kcal | Carbohydrates: 37g | Protein: 6g | Fat: 5g | Saturated Fat: 1g | Cholesterol: 33mg | Sodium: 244mg | Fiber: 6g | Sugar: 17g
Keyword : Flax Carrot Apple Muffin


Flax Carrot Apple Muffins | Healthy Ideas and Recipes for Kids

Natalie Monson

I'm a registered dietitian, mom of 4, avid lover of food and strong promoter of healthy habits. Here you will find lots of delicious recipes full of fruits and veggies, tips for getting your kids to eat better and become intuitive eaters and lots of resources for feeding your family.

Learn More about Natalie

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Recipe Rating


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!

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!

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.

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.

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?

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!

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?

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?

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

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.

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.

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!

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

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!

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!

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!

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!!

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.

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!

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!

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.

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.

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!

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.

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

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!!!

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.

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!

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 🙂

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! 🙂

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!

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? :/

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!

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

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!

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!

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.

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.

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.

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.

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?


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!

5 stars
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

5 stars
Hi I tried you recipe .The muffins are great.I just used oatmeal instead od grinding the oats and I forgot the baking powder. I used half raisons and half cranberries
.Because thats what I had.I didn’t have any carrots but the muffins still are good.The next time I will get the carrots and remember the baking powder. Thanks so mu h for this recipe.

I made these for my autistic granddaughter – she is very fussy but she loved them; they kept for three days and I thought they tasted better the next day.

Mine are baking right now. I tweaked the recipe, hoping to drop the carbs. If it works I’ll post my changes. I am interested in finding out how many carbs are in one of these, as written. Thank you.

5 stars
I just tried one of my muffins. Wow, so moist and delicious. Being diabetic I tried to bring the carbs down as much as possible. I substituted in almond flour, almond milk, I left the apples in a very small diced size and I also used granulated baking splenda. No carrots, no raisins. Amazing, thanks for the starting point recipe. They aren’t as pretty as yours, but they taste great.

4 stars
thanks for the yummy recipe! but what will make it the best for me is if it’s Keto Friendly whoaa! Can’t wait to try

5 stars
I am writing this after 1 month actually I forgot to write it before but I would like to tell you, I tried these muffins for 2 kid’s and they both were super happy after having it.

Thanks for sharing the amazing recipes with us.

5 stars
made these tonight. i didnt have whole wheat four so i use all purpose and fid not use or substatute the cranberries. my 6yr old n i love them. my husb n 5yr old said not right now. l will make again in future and make a double batch!

Hi Megan! I haven’t tried this substitution myself but it would probably work. Your batter might be a bit thinner in consistency but I would think the muffins would still turn out. If you try it, let us know how it turns out? Thanks!

3 stars
These really need 1/4 tsp salt and a little healthy fat like some coconut oil – kids need a little fat for their developing brains!

Hi Tanya, you can definitely try this substitution! It usually works as a 1:1 substitution. I would go with maple syrup (honey can sometimes result in the bottoms turning overly brown.) Good luck!

My family loved these! I was out of oats so I just used 2 cups gluten free flour and the flax. Great recipe!

The recipe says, 3/4 cup flaxseed, ground. ” I interpret that to mean measure 3/4 cup of flax seed and then grind it. Is that correct? Or should it be “3/4 cup ground flaxseed,” measuring it after it’s ground? In other words, is it 3/4 cup flaxSEED or 3/4 cup flaxseed MEAL?

Has anyone had success making this recipe gluten free with a simple gluten free flour blend substitute? I usually use Bob’s Red Mill all purpose gluten free blend.

5 stars
I made these tonight and my kids and I love them! I baked them in a mini donut pan as well as a muffin top pan, both came out perfect! I also subbed half of the carrot with sweet potato, just to use up some that I had on hand, and it turned out great! The muffin tops were like a healthy substitute for Panera’s pumpkin muffies, just perfect!

Hi!!! I was looking for a healthy recipe for my daughter’s first birthday, and I came across your recipe! I’m so excited… I bet it’s very delicious!
If I were to bake it in a cake pan instead, how much time would you recommend?
Thank you!!!!

Hi Aline, I’m not sure about the time in a pan, but you could start checking on it after 20 minutes or so. 🙂

5 stars
Love these muffins! A little time consuming to make but if you use a food processor for the apples and carrots it really speeds it up! I followed the recipe exactly but omitted the cranberries. I usually find muffin recipes too sweet and have to cut the sugar back but these had perfect amount of sweetness to them! My kids seem to like them, I’ll definitely make them again!

Hi–has anyone made these using baby food? The thought of manually shredding all of this sounds daunting. If you think it would work, do you think it would be a 1:1 substitution for the shredded carrots/apples, or maybe less? Thanks!

We haven’t tried that before! The moisture content would be different- but you could certainly try! Using a food processor to shred it helps speed things up for us too!

5 stars
My almost 3 year old LOVES these muffins. They are a great way to get fiber into her day, and she loves the taste of them. The first time I made these they felt labor intensive, but the second time I used bagged oat flour and put the apples and carrots in my food processor instead of hand grating and they were easier to whip together. Great recipe!

5 stars
These are so good !! Followed the recipe to a T. I was surprised they would be so moist because there’s no oil in them… but guess the fruit/veg keeps them moist.
I’ve made plain apple with sultanas too, and swapped sugar for honey. Also really nice. Great recipe and full of goodness for the little ones !!! Freeze super well too. Zap them in the microwave for 1min and a warm & healthy snack is ready for them.

Tweaked recipe just a touch, added walnuts and banana to it, replaced cranberry for regular raisins….. house smells divine this morning. Thank you for whoever posted this recipe originally. Cheers from Regina, Canada…?

5 stars
Do these muffins require refrigeration? We plan to eat them within about 3 days. I just made the recipe, and they taste great. I needed to cook them for about 17 or 18 minutes, for regular size muffins. It made 18 muffins. Thank you for the recipe.

4 stars
I love the flavor, I added 1/2 tsp. Apple pie spice as well and changed brown sugar to palm sugar.
I am disappointed that they do not come out of the paper wrapper, not sure if anyone has had that issue. Could it be because there is no oil added? I only get the top half of the muffin.

5 stars
these are really great, I doubled the recipe and subbed almond flour for the flax and added chopped walnuts and some chia seeds, made a honey, butter cream cheese spread for them