Whole-Wheat Carrot Applesauce Muffins

148 Reviews / 4.8 Average
This recipe is by far the new favorite muffin in our house. Move over blueberry, zucchini, and even pumpkin—these are so deeelicious and could be eaten with breakfast, lunch, or even dinner (maybe as a side to some fall soup?)!
↓ Jump to Recipe
Carrot Applesauce Muffins from 100 Days of #RealFood
Featured Comment

it was a HUGE hit with all three of my kids! Thank you for this recipe. It is in regular rotation and gets rave reviews every time!
– Ashley Oswald

For those who are looking for cupcakes for little ones (i.e. smash cake) I would totally top one of these off with some homemade unsweetened whipped cream and call it a day. This would be perfect for your baby! And if you prefer to avoid honey for your really little ones I think 100% pure maple syrup would work just fine as a substitute.

Posts may contain affiliate links. If you purchase a product through an affiliate link, your cost will be the same but 100 Days of Real Food will automatically receive a small commission. Your support is greatly appreciated and helps us spread our message!

742 thoughts on “Whole-Wheat Carrot Applesauce Muffins”

Leave a Comment

Your email address will not be published.

Recipe Rating

  1. These are WONDERFUL! I just add a bit more spice than called for, slightly more vanilla and toss in some chopped pecans. My kiddo and I LOVE them! So fast to make. I can literally whip these up in no time.

  2. 5 stars
    Made these for the first time today and they turned out amazing! I used maple syrup instead of honey (cuz I had a Costco sized bottle!) and coconut oil instead of butter (again, cuz I had a Costco container) and added a handful of chopped pecans too. My toddlers loved it, so these will become a regular. Thank you so much!

  3. 5 stars
    I’ve made a modified version of this twice now with huge success! Our favorite version: maple syrup instead of honey, 1/3 c coconut oil instead of 1/2 c butter, add a few handfuls of raisins, and a handful or two of walnuts, finely chopped. Thanks for the inspiration! I love this site.

    1. Oh, and I make mini muffins instead of full size. Eating a couple of them feels like more of a treat to me than one big muffin, even if I know it’s just an illusion! ‍♀️ I was surprised to find that I still needed to bake them the full time.

      1. I don’t think that would turn out well, I would recommend finding a muffin recipe that’s already been adapted without eggs.

  4. 5 stars
    We love these!!!!! How many muffins are a serving? I am meal prepping so I want to calculate caloric intake. Thank you

  5. Tried this with a full cup of grated carrots and maple syrup instead (1:1 ratio) of honey and turned out great! Had to leave them in the oven for probably 30 mins or so. tastes very healthy and not too sweet.

  6. 5 stars
    So delicious !!! Love eating them warm with butter (probably not the healthiest) but they are whole wheat! (I didn’t include the carrots, one of these times I’ll take the plunge) Thank you for the yummy recipe!

  7. 5 stars
    This is a staple in our house! We always have some on hand in the freezer. I used to make these with maple syrup when my son was under 1 and for his birthday this was his smash cake! These are perfect for snacks or breakfast on the go!
    Quick question, has anyone tried using whole wheat pastry flour for this recipe? I can’t get white whole wheat flour in my town and I’m waiting for it to come in the mail but we have a hankering for these muffins!

    1. We haven’t tried it with pastry flour yet, it may just give it a slightly different texture though. Let us know! – Nicole

      1. They are not the same. Whole wheat pastry flour has a lower protein content. It’s softness makes it great for things like pancakes, waffles, crepes, scones, biscuits, etc. For anything that needs structure like yeasted whole wheat bread, pasta or cake, stick with white whole wheat flour. If you only plan to buy 1 kind, stick with white whole wheat as it can be used in any application.

    1. Hi Katie, that should be just fine…maybe just decrease the amount of cinnamon you add in the beginning unless you don’t mind the taste. Should come out yummy either way! – Nicole

  8. 5 stars
    Just made these for a snack to take to a play date
    I doubled the recipe and used 3/4 coconut oil and 1/4 olive oil
    Was generous with the grated carrots (prob about 2cups)
    Used 1/2 tsp all spice
    1/2 tsp nutmeg in place of ginger
    Sprinkled a dash of dark brown sugar on top before baking
    They turned out so moist and delicious

    Thanks so much!

  9. I really like using instant pot for baked goods because 1) it makes a more reasonable portion for a family and 2) hello -Instant Pot which means I can close the lid and walk away.

    Any suggestions to make in Instant Pot? Thanks for all the great recipes!

    1. Amy Taylor (comment moderator)

      Hi there. We’ve never attempted to make a cake from this. I’d hate to give you bad advise on such an important cake! ;)

      1. 5 stars
        Do they taste as good with the maple syrup? Want to make these tomorrow but need to get honey. Have maple syrup on hand! Love them with the honey!

  10. 5 stars
    Have made these multiple times and they are always a huge hit!! I typically have to make more than one batch.

  11. Made these muffins today and my entire family loves them! All 3 kids and hubby approved and asked for me to make them every week. Thank you for a great recipe!

  12. Wonderful recipe!! I followed the recipe exactly, other than added about 1/4 cup coconut flakes. Turned out beautifully. Saving this recipe for sure!

  13. I followed this recipe with all the necessary ingredients but added raisins and chopped apple. The batter was very different than white all purpose flour and almost seemed fluffy and when the muffins were done they came out dense and seemed to have a doughy taste, no matter how long I cooked them. This was my first time baking with white whole wheat, so I’m not sure if this texture is just common for that type of flour. Next time I might try doing half and half.

  14. These were delicious! I added a little extra carrot because I had so much to use and 1/2 cup oatmeal. I will be making these again!

  15. I know you don’t post nutrition information, but I am an insulin dependent diabetic. I need to know how many carbs are in what I eat so I can take the right dosage of insulin. Any advice on how to calculate this recipe?

  16. Hi there I was just wondering if I can use anything to replace the honey? Maybe 100% maple syrup? And if I did this how much would I use I wonder?

  17. I love this recipe!!! Muffins turned out perfect.
    I had no carrot so added 1 cup of frozen rasberries and 1 cup of coconut and they are so delicious!!!

  18. what would be a real food sub for the butter. My son can’t have milk products or eggs. The egg i am good on it is just the butter i am not sure how to sub that and have it be not highly processed.

  19. 5 stars
    These are SO good Lisa! I’ve been playing around with adding yogurt to recipes in place of oil, so I added plain greek yogurt in place of the butter, and threw in 1 c. chopped pecans. Excellent breakfast muffin! :O)

  20. Nancy Williams

    5 stars
    These are so good!! I even replaced the butter with coconut oil. Great to have on hand for a quick snack or breakfast on the go. Thanks!

  21. I want to make these but don’t have any carrot shreds at the moment. I do have a jar (4oz) of pureed baby food. Can I add that instead? I wasn’t sure how leaving out the carrots would change the consistency, and if I should add something in to account for that.

    1. Amy Taylor (comment moderator)

      Hi Erin. We’ve not tried pureed carrots in this recipe. Let us know how it works for you.

  22. I just made this recipe as mini muffins with maple syrup and grated Apple instead of applesauce. I used only 1/2 the ginger and it tastes awesome!! It’s sweet without being cloying. Great recipe for kids. I got 24 decent sized mini muffins. Much easier for adult portion control.

  23. 5 stars
    would love to try – i dont see baking powder ? is that my istake?
    also can I make this in a cake pan instead of as muffins? what would I adjust? TIA

  24. Do I keep these out or do I have to freeze them? I wanna know how long they will last on my counter…

  25. 4 stars
    I have made these twice this week. Both times they bake up beautiful but once I pull them out to cool they sink in. The only adjustments I made were (1st batch I cut the butter in half and did whole fat yogurt and adjusted the spices) (2nd batch I just adjusted the spices). My applesauce and vanilla are homemade, I used King Arthur whole wheat white flour. I just don’t understand. The flavor is fine but they seem under cooked in the middle. I even baked them an extra 6-7 minutes. Any thoughts? My baking soda is not expired.


    1. Amy Taylor (comment moderator)

      Hi. Mine often sink just a little, too, and I typically cut the butter. :) I think any adjustment in the ingredients can have a slightly different outcome.

      1. After doing some research I discovered that my baking powder (which I had used by accident) had gone bad. It doesn’t expire until July but I tested it and sure enough it was bad. So my next batch turned out great…along with some the banana -pumpkin bread I made yesterday.☺️

        Thank you!!!

  26. 5 stars
    Love these! Used half a teaspoon of pumpkin pie spice instead of ginger and they were so good! Also used whole wheat pastry flour. My 3 year old loves them. Also used 1/4 cup of whole yogurt for half the butter as suggested by another commenter.

  27. 5 stars
    Does Lisa use the organic white whole wheat flour? I can find the regular white whole wheat flour but I am having a great deal of trouble finding it organic! I try to buy as much organic as possible, so just wondering if organic flour would be considered a necessity since I am having trouble finding it! These muffins are absolutely amazing though!! I have made them a few times and myself and kids love them!

    1. Amy Taylor (comment moderator)

      Hi Amanda. Lisa does try to buy organic whenever possible but it is certainly not required. ;)

  28. 4 stars
    These took quite a bit longer to bake than the time given (28min) even though my oven was on 180C. Maybe the time indicated was for the convection setting. I added a 1/4 cup wheat bran for extra fibre and a pinch of clove powder for extra spice. My kids and I didn’t find them too gingery at all. They taste quite good – moist and favourful.

  29. 3 stars
    The texture of these muffins is fine moist, but better with half unbleached flour and half whole wheat. Makes a lighter quality muffin. Way too much ginger , Really spoiled the whole thing, having a bitter after flavor that lingered on the tongue. Perhaps 1/4 tsp or even 1/8 tsp ginger would work better. You could replace half of the butter with 1/4 cup of plain yogurt for less calories and nice lemony flavor, especially if you reduce the ginger.

    1. I have made these numerous times without ginger and they are wonderful! Try not using it at all and see how you like them! Also, try white whole wheat flour instead of regular whole wheat flour – it made a huge difference when I made the switch! That way you do not need any of that processed unbleached flour! = )

  30. Not a fan of these muffins. I used half the amount of ginger and did everything else exact but the ginger taste was still too strong. Also, not really that healthy considering it has 1 stick of butter in it!

    1. 5 stars
      I can’t understand why you wouldn’t like these muffins. They are delicious. 1 stick of butter is not bad over 12 muffins.

  31. Hi! This is my daughters favorite muffin recipe, and I’m going to use it for her birthday cake. Of course, a cake needs frosting, and I’m not sure what would taste good. Any suggestions? Thanks!

  32. 5 stars
    Wonderful! I used 1/3 C honey and whole wheat pastry flour. They are so moist and fantastic flavor. Forever in the recipe archive, this one!

  33. Sooooo good! I used maple syrup instead of honey, and only 1/4 cup. Threw in some raisins too. These will be a lunchbox staple for sure!

  34. 5 stars
    Love this recipe. A sweet muffin that is whole grain and all real ingredients. Great preschool snack! My whole family loves these muffins!

  35. 5 stars
    OMG! I just tasted the muffins and they are soooooooo delicious! Thanks for the recipe. I added the whip cream and my daughters loved them as well.

  36. Would a couple of apples pureed in my vitamix or the blender (to equal 1 C, pureed) work? I live overseas where we don’t have applesauce. I’m always concerned that there might be more liquid when it cooks.

    1. Hi Cindy. I’m not part of the blog team, but if you have access to apples, a pot, and and a stovetop, you can make your own applesauce! Peel, core, and chop up the apples, then put them in a covered pot over low heat for 20-25 minutes, until the apples are nice and soft. Purée in your blender or using an immersion blender, and voilà! Applesauce.

  37. Love these muffins!!!! Just wondering how is the best way to store these homemade goods and how long should they last?

  38. I’ve made four batches of these in the past week because my family loves them so much! Today I used blueberries instead of carrots and they turned out great. Thanks for the yummy and healthy recipe! Love your site!

  39. 5 stars
    I made the cake version of this recipe for my daughters birthday, she asked for a cake that “Daddy could eat”….we had to change a lot of his diet because of his Lyme disease. So this was a great recipe for no sugar. I also added pineapple and walnuts and made the icing in the cookbook! It was a HUGE hit and for once everyone’s plate was licked clean, although I think the little one went around and licked it for them. Thanks for the awesome recipe :)!

  40. I have ripe bananas I need to use up, think I could sub in the bananas for the apple sauce? Also, I don’t have enough butter in the house and I usually bake with yogurt. Do you think I could sub in yogurt (full fat) for the butter? Would it be a 1:1 swap? If I can’t I can always use coconut oil but my kids don’t like milk so I try to sneak dairy into their food for the calcium. Thanks!

  41. 5 stars
    I love all of these recipes and lunch/snack ideas. Do you have a recommendation for great containers for freezing muffins? I usually make 2-3 different kinds one weekend and freeze them for the kids to pick for their snacks during the next few weeks.
    Thank you

    1. Amy Taylor (comment moderator)

      Hi Barbara. I usually use large Ziploc bags, removing as much air as I can with a straw. Large plastic Ziploc containers also work well but I think the bags do better at preventing freezer burn.

  42. So, we have some carrot baby food jars on hand…how would I substitute that in for the shredded carrots? Or would you not recommend that?

    1. Amy Taylor (comment moderator)

      Hi there. We’ve not tried to use a puree. I think it will work nut may change the texture a bit.

  43. Could coconut oil be used in place of the melted butter and spelt flour in place of regular whole wheat? Excited to try this one!

    1. I made a batch today and used coconut oil instead of butter (which I’ve always used in the past). They turned out fine!

  44. 5 stars
    I grate a lot of carrots and freeze packets for when I make these. Also, I use less butter and substitute some ground up oatmeal (in food processor) for flour. Recipe is very forgiving.

  45. 2 stars
    do you have two different versions of this recipe? I made a slightly different recipe several months ago. The other recipe didn’t have an egg in it and they were fabulous! I tried this recipe tonight and I had the same problem other bakers did – collapsed in the center and a bit mushy. Not sure where I went wrong.

  46. Martha Nethers

    5 stars
    I just made these yesterday with homemade applesauce and carrots from my garden. YUM!! Thank you for all you do!!

    1. I broke down the calorie count for each ingredient. It comes out to about 180 calories per muffin making 12 muffins.

  47. The wheat germ + white flour really worked out just great! I usually have whole wheat on hand, but didn’t that day. The muffins disappeared pronto!

      1. Hi! I have made these twice for my daughter and a few other toddlers, and they all have loved them!!! Do you know approx. how many carbohydrates and sugar each muffin has? Thanks so much!

      2. Amy Taylor (comment moderator)

        Hi Kristen. No sorry. We do not provide nutritional breakdowns for the recipes. We just want folks focusing on getting the processed stuff out of their diets. :)

  48. These were delicious! I had to make two substitutions. I only had 1/2 c applesauce, so I grated an apple along with the carrot. And i was out of whole wheat flour, so I used 1 1/4 c white flour plus 1/4 c raw wheat germ.

  49. Any idea how long to bake these for if I decided to try the mini muffin route instead of regular sized ones? Thank you!

      1. How many mini muffins do you usually get out of this recipe? Hoping to make them for my son’s preschool class snack and am curious if I need to double the recipe or not.

  50. Do these have the same texture as a traditional cupcake? I want to make carrot cake (or cupcakes) for our unhealthy extended families on Easter but don’t want it to seem like a muffin or else they won’t eat it! I want them to taste it, like it, and then for me to tell them how much healthier it is. :) Thanks!

    1. Amy Taylor (comment moderator)

      Hi there. Sorry that I didn’t get to this before the holiday. I hoped you tried it. These are my family’s favorite! :)