Whole-Wheat Carrot Applesauce Muffins

148 Reviews / 4.8 Average
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Carrot Applesauce Muffins from 100 Days of #RealFood
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This is a staple in our house! We always have some on hand in the freezer. These are perfect for snacks or breakfast on the go!
– 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.

Carrot Applesauce Muffins from 100 Days of #RealFood

Whole-Wheat Carrot Applesauce Muffins

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?)!
148 Reviews / 4.8 Average
Prep Time: 10 mins
Cook Time: 22 mins
Total Time: 32 mins
Print Recipe
Servings: 12 muffins



  • Preheat your oven to 350 degrees F. Line a muffin pan with paper, foil, or silicone liners, and set aside.
  • In a medium bowl whisk together the flour, baking soda, cinnamon, ginger, and salt.
  • In a large bowl fitted with an electric whisk (or beaters), mix the butter, honey, egg and vanilla together on medium speed. Turn the speed down and slowly add in the flour mixture until well combined. The batter will be fairly thick at this point.
  • Using a spatula, carefully fold in the applesauce and carrots (I used a cheese grater to shred the carrots). Divide the batter evenly among the muffin cups. Bake for 22 to 24 minutes or until a toothpick comes and muffins are beginning to turn golden brown on top. Enjoy!


We recommend organic ingredients when feasible.
Nutrition Facts
Nutrition Facts
Whole-Wheat Carrot Applesauce Muffins
Amount Per Serving
Calories 179 Calories from Fat 72
% Daily Value*
Fat 8g12%
Saturated Fat 5g31%
Cholesterol 34mg11%
Sodium 267mg12%
Potassium 70mg2%
Carbohydrates 25g8%
Fiber 2g8%
Sugar 14g16%
Protein 3g6%
Vitamin A 1600IU32%
Vitamin C 0.7mg1%
Calcium 19mg2%
Iron 0.5mg3%
* Percent Daily Values are based on a 2000 calorie diet.
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741 thoughts on “Whole-Wheat Carrot Applesauce Muffins”

  1. My family loves these. I have made them with coconut oil instead of butter and maple syrup instead of honey and they turned out great. I have also used ground flax mixed with water instead of an egg and added shredded apple(with the carrot), still turned out great. It’s a wonderful recipe.

  2. My daughter isn’t getting enough Vitamin D, and I heard that Greek yogurt was a good substitute for butter. I was thinking of replacing the butter with fortified Greek yogurt and replacing the applesauce with shredded apples. Any thoughts on how this would turn out? I don’t have the best instincts when it comes to baking. Sorry if a question like this was already asked, and thanks in advance for any response.


  3. 5 stars
    These muffins are my new obsession right now!! I can’t stop eating them! Oh and my 20 month old son loves them! He eats them for breakfast or a snack.

  4. Would like to make 1/2 or the recepie. If i use 1 whole egg for the 1/2 of the recepie, what other ingridients should i adjust to keep the right dough consistency?

  5. I just wanted to say that I just made these tonight but because I didn’t have any applesauce I used puréed/pulsed beets with a little squeezed orange to make the consistency similar to applesauce and it turned out great! Thank you, I will definitely beaking again

  6. I made my own chinky applesauce with peeled apples, water and cinnamon…then added to the mix with organic carrots. DELICIOUS!!

  7. Just made these with maple syrup instead of honey so my baby could eat them. They are amazing!!! Best muffins I have ever made. Thank you!

  8. 5 stars
    OMG!!!! These muffins are AMAZING! my kids think they are candy muffins. We are calling them love muffins, since they love them so much. It is the first thing in three years to get my 6 year old to not choose a frozen blueberry waffle (he eats three of these instead!).

  9. Oh. My. These were just too delicious to even articulate. Moist, flavorful, absolute goodness! I will try with coconut butter instead of oil since I try to be dairy free – but following the recipe directly, just wonderful!

  10. Excited to try these! looks so simple. Just a general question on baking with coconut oil. Do you typically melt the oil first?

  11. I’m wondering if anyone has tried this substituting the Wheat flour for the alternative (coconut/almond flour) for those who are gluten or grain free? If so what measurements did you use and did you have to add or subtract any ingredients to make it work?

  12. 5 stars
    I made these last week for my Monday morning client. She wrote to me and told me that these were, by far, their favorite muffins that I’ve made in over a year and a half of cooking for them. THANK YOU! I omitted the egg, because she didn’t have any in her refrigerator. ;)

  13. 4 stars
    For high altitude families… I removed 1T of honey and added 2T of applesauce. Increased backing temp to 360F and took the muffins out promptly at 22 min. I used a greased (Crisco) muffin pan & removed the muffins right after taking them out of the oven, cooled on a cooling wrack so the outsides don’t get to crusty. Love them.

    1. 5 stars
      I live in high altitude (about 7,600 ft.) and I made these according to the recipe except they only had to bake for 15 minutes. They turned out perfect!!!

  14. Quick question. I noticed that in some of the recipes you specify that you use king Arthur’s white whole wheat flour. Do you typically use that when the recipe calls for whole wheat flour? For example your wheat bread. Do you use white whole wheat?

    1. Amy Taylor (comment moderator)

      Hi Erin. Lisa mostly uses straight up whole wheat but the white whole wheat is always and option, especially if you are just transitioning or prefer a lighter taste and texture. ~Amy

  15. I loved the sounds of this recipe, however when I tried itI loved the sounds of this recipe, however when I tried it today, the muffins didn’t rise, in fact they kind of caved in. I tried cooking them longer but they just ended up starting to get burnt. When I finally took them out, the middles were raw. What happened??? I followed the directions exactly so I don’t know what it would have been! can baking soda go bad? I’ve had it for about a year and a half? today, the muffins didn’t rise, in fact they kind of caved in. I tried cooking them longer but they just ended up starting to get burnt. When I finally took them out, the middles were raw. What happened??? I followed the directions exactly so I don’t know what it would have been! can baking soda go bad? I’ve had it for about a year and a half?

    1. Amy Taylor (comment moderator)

      Hi there. It is important to use all fresh ingredients. Any old ingredients could contribute to a recipe not working correctly.

  16. These are very good muffins. I made a few alterations and thought I would share in case anyone else is pondering similar modifications. I doubled the recipe but only used one stick of butter (1/2 c), substituting 1/4 c of plain yogurt for the rest of the oil. I also used only 1/2 c of honey, adding an extra 1/2 c of applesauce to make up the difference. They turned out great. They are especially delicious with some cream cheese on the top! I think using the full amount of honey would make them a great cupcake substitution. With half the honey they were plenty sweet for a snack or breakfast.

  17. I made these yesterday and these muffins were amazing. I’m making more today so that I can freeze them. Thanks for this recipe!

  18. This recipe is amazing!!! I’m Lucky if they last 2 days in my house between my husband, 2 girls, and I. Thank you for the delicious recipes!!!

  19. 5 stars
    I made these last night for breakfast this morning, and my 3-year-old loved them! They are so moist, and just sweet enough. I didn’t have ginger on hand, so I used lemon zest instead. Was very good, but I’d be curious to see the difference with the ginger. Next time I will add raisins and walnuts for extra texture. I love your site, and every recipe I’ve tried from your book has been delicious!

    1. Amy Taylor (comment moderator)

      Hi Tess. I guess I would use (and re-use and re-use…) individual small zipper bags or sandwich bags for one or two muffins, removing the excess air from each bag. With zipper bags, I use a straw to suck out the air. :)

  20. Hi I am not seeing the carrot cake recipe online but am using the recipe in the book. I used the cook time and its not done… will cook longer but curious since the recipe is not onine if maybe the cook time is not correct? Any insight is appreciated. Thanks and love the book!

  21. 4 stars
    I made these yesterday afternoon and absolutely loved them! The flavor was amazing, especially for something without sugar and with whole wheat. I let them cool completely, even longer than usual, then put them in a tupperware container. When I woke up today, the carrots that were close to the surface of the muffin had turned green! Is this normal? Is this mold? I went through a some of the comments and didn’t see anything. I used a store bought bag of matchstick carrots so worried maybe they were too big? I want to make these again, but want to make sure it isn’t mold!

    1. Amy Taylor (comment moderator)

      Hello Opal. Carrots sometimes oxidize when they come in contact with baking soda which can result in the green color.

    1. Amy Taylor (comment moderator)

      Hi Tina. I typically freeze these if I need to keep them past a couple days. The fridge tends to dry them out.

  22. 5 stars
    I made these today and they were a hit with my kids and husband!! My husband wants me to make a double batch to bring to his office! On a side note, do u know if u can use coconut flour instead to make them gluten free?? Thanks!!

    1. Amy Taylor (comment moderator)

      Hi Candace. You can certainly experiment with different flour combinations in order to make a gluten free version. You could not substitute coconut flour 1:1, however, because it is very different from wheat flour.

  23. 3 stars
    They’re OK, but a bit boring and are more cake-like than muffin-like.
    The recipe supposedly makes 1 doz “oversized” muffins? It actually makes 1 doz regular-sized cupcakes.

  24. I’ve tried these twice and both times the outsides are cooked fully, but the inside is all mushy and wet. Maybe they’re supposed to be? Or maybe I need to squeeze the moisture out of the carrots?

    1. Amy Taylor (comment moderator)

      Hi there. Ovens can vary as to how they cook. You may want to cook a little longer and reduce the temperature a little.

  25. Would these still have that muffin/cake like fluffiness if I just eliminate the honey (or maple syrup)? I want to use this recipe for my daughter’s smash cake, but because I’m trying to encourage less sweets I only want it sweetened with the applesauce. Thanks!

    1. Amy Taylor (comment moderator)

      Hi. We’ve not tried eliminating the honey. If you add more applesauce in its place, I think it would work okay.

  26. I just made these – but had to sub the whole wheat flour with 210g of gluten free flour due to an intolerance in our household. Let me just say, my house smells amazing! My 4 year old had a blast helping me. AND they taste GREAT!!!

  27. 5 stars
    I subbed parsnips from our CSA box for the carrots and the muffins were a huge hit with my kids! I also added in some nutmeg which was a nice touch. I make the original version on a regular basis for my preschooler and baby. Love how moist they are!

  28. 5 stars
    Love these muffins and have made many times as regular muffins, mini muffins and mini loaf breads. I used coconut oil this time and it seems the carrot flavor is more pronounced. Definitely like butter in these ones better. The one draw back on these muffins for me is the time to grate carrots. I pulled out my kitchen aid mixer and grater attachments and made enough extra grated carrots to freeze 3 double batches so we will see how the frozen carrots work out. i plan to fully thaw before adding. I always double this recipe and get 30 regular muffins. I have made these for non foodies and have always received compliments. I think this is one that anyone will enjoy! Thanks! Keep them coming.

  29. I cant see the recipe on the website. Has it been moved or is there something wrong? I have tried google crome and internet explorer

    1. 4 stars
      I used 1/2 cup grape seed oil instead of butter and it worked really well. I also substituted sugar for 1/3 cup honey and added 1/2 a grated apple. Lovely and moist.

      1. Thanks for the substitution info! I have used Earth’s Balance in all of Lisa’s muffin recipes and it has worked perfectly (one of our children has a milk allergy so real butter isn’t an option). I’m out of Earth’s balance and was glad to find that grapeseed oil works!

  30. I have made these before and they came out great, but it’s been a while. I made them last night, following the recipe exactly, only doubling the ingredients, and they didn’t come out so good. I thought they were done, however once they were cooled and I tried them, they were very moist in the middle. I did some large and some mini muffins and even the mini muffins were not done in the middle. I don’t know what I did wrong :(

  31. These might be the best muffins I have ever made! My 3 yo and 18 month old LOVED them! Do you think it would adapt well to a loaf? How would that change baking time? Thanks!

    1. 5 stars
      I baked them as 36 mini-muffins for 22 minutes and it seemed to work out just fine. They are disappearing fast ! Quite popular with both my 4 year old and my 5.5 year old.

  32. These are so good! First batch of whole wheat muffins the family is devouring as I type ;)
    I did use half honey/ half maple syrup for a double batch and used pumpkin spice seasoning because that’s what sounded good. Definitely will become a staple in our house! Thank you.

  33. Just made these this afternoon, they were so moist and I liked also that they werent super sweet! I dont even like carrots and these were delicious.

  34. 5 stars
    These muffins are awesome. I’ve made them a few times with and without adding raisins. They are so moist and have a wonderful flavor. My kids love them and don’t complain about the carrots. The entire batch barely lasts 24 hours.

  35. These muffins are delish! I had no honey on hand so used maple syrup. I love the flavor and that they aren’t super sweet. Hope the kids like them tomorrow!
    Thank you for such a wonderful blog! I am slowly trying to convert myself & my family to healthier baked goods and more real foods.

  36. These were delicious!! My kids love them. I doubled the recipe and made mine mini muffins, which are the perfect size for little hands! We froze some and we’ve been eating the rest warmed up for breakfast before school.

  37. Why so much honey? There is no reason to have that much as applesauce is naturally sweet. I was surprised at this. I only added 1/4 cup and thought it was still too sweet.

  38. Is there a substitute for the honey? I would like to make these for my 14 month old, but I’m not comfortable giving him honey yet. Thanks!

  39. Hi! I only have fresh ginger root on hand, not ground ginger. Does anyone know if I could substitute this instead? If yes, what amount?

  40. I’ve got a batch of these in the oven right now and due to the previous comments regarding “mold” – I researched the fact. What I found was that the baking soda can throw off the pH of the carrots and cause a reaction that turns the carrots green. There is no cause for concern (assuming you’re not using old carrots to begin with). Here’s one of the sites I researced (http://www.thekitchn.com/food-science-when-good-carrots-52210). Please do your own research if concerned. I can’t wait to try these. :)

    Hope this helps!

    Holly W.
    Portland, OR

  41. I love these muffins! However, when I get some out of the freezer and let them thaw, the very next day they have mold on them. Is there something I’m doing wrong? Should I leave them in the freezer bag to thaw? Or let them sit out in open air on the counter? I don’t know what I’m doing wrong!

    1. It may not be mold. Are you seeing green in the muffin? I thought the same thing at first and researched and realized it was a reaction that can sometimes happen with baking soda and the carrots. Just giving you a heads up that this could be what it is.

    2. Assistant to 100 Days (Amy)

      Hi Hanna. Ditto to what Tori said. Mold should not be happening that quickly. Typically, I throw frozen muffins into lunch boxes or thaw them in the bag in the fridge overnight. ~Amy

  42. Yummy! Just made these on a cool Fall day. I added currants to them and had to try one right out of the oven. I would rate them 5 stars but it would not let me.

  43. I’ve made these before and everyone loved them, my husband and his brother fought over the last one! Definitely my go-to muffin recipe, very versatile too.

  44. These are absolutely delicious! Made them for the first time today. I love the fact that they are a real food. Thanks for the recipe.

  45. Hello,
    We have always been a health conscious family but just recently i decide to switch us to only eating REAL food and starting to make everything from scratch instead. I was wondering what you do to save time? I prefer to make things in big batches and then freeze if possible. This works well with our bread and pancakes etc. Can I do this with the muffins or do they thaw out too soggy? I would hate to freeze a whole batch to find out it doesn’t work! Thanks!

    1. Assistant to 100 Days (Amy)

      Hi Rachael. Lisa cooks and freezes regularly as well as uses leftovers. These muffins freeze well. They are very moist and moist when thawed but not soggy. ~Amy

  46. 5 stars
    I just made this as a cake (from your cookbook). The cake turned out wonderfully, but the cream cheese frosting curdled! :( I followed directions, but have you ever had this happen? It didn’t whip very long before beginning to curdle, if that helps. I would love to try the frosting again and be successful!! :) Thanks in advance.

    1. Assistant to 100 Days (Amy)

      Hi Mandy. Room temp cream cheese is less likely to curdle when you whip it up. Could that have been it? ~Amy

  47. 5 stars
    I just made these, but I didn’t have any honey so I used half as much molasses instead and crossed my fingers for the best LOL! They turned out amazing!!! My 8 year old son just ate 2 in a row and said they were delicious! Thanks for the awesome recipe! :)

  48. Just wanted to let you know I made these for my 3yo and 1yo and both really liked them! I made them into mini muffins. I simply baked them at 350 for 15 minutes. Thank you!

  49. 5 stars
    Lisa! The kids DEVOURED these! I was able to sneak one, one- and I had to sneak it. They loved these and I loved how wholesome they are (well, were). We are off to the store to buy more carrots, because they want to bake another batch! We tried substituting 1/2 cup of coconut flour for whole wheat, and using coconut oil instead of butter (BJ’s had a sale on both) – so delicious! Thank you again for creating this REAL FOOD muffin.

  50. This recipe is beyond delicious!!! My husband whined while I was preparing “morning glory muffins”. And I thought, oh raisins would be so tasty in these muffins. I was right and since my 2 year old twins love “rais” I can’t wait to pack these in their lunch box tomorrow! Thank you so much for another nutritious, family friendly recipe. This will definitely be part of our rotation! (And although hubby might not be keen on these he loves the blueberry muffins :-)!

  51. 5 stars
    I just wanted to give a quick thanks for this recipe! We have two year old twins and (sorry to say) we’re not a super health conscious family yet but trying to take baby steps to improve. We’re going on vacation next week and I was looking for a recipe to bake up some easy breakfast muffins to take along. I was searching for applesauce as I had it on hand and figured it was easier than chopping fruits. I got so lucky to fall upon this recipe! We had everything on hand (even including the whole wheat flour and pre-shredded carrots) and it was a breeze to whip up. The true joy? My two year olds LOVED them and kept saying “mmmm mmmm.” Five stars all around!

  52. Hi, these look fantastic! How do you make applesauce? It’s not a common ingredient here in England. Also have you ever considered writing your ingredients in other ways, I.e in UK we use lbs/ozs or grams and its really hard to convert to cups! Icups aren’t really used here.

  53. Hi Amy!

    Thank you so much for posting this recipe. I’ve started using whole wheat flour this past week as part of having the family eat more healthy. This is an amazing carrot muffin recipe! I made it as directed and it came out so well! Hubby has taken three to work this morning and my one year old devoured it in one sitting :) Thank you once again and here’s to many more delicious recipes to come! Cheers!

  54. Is honey and maple syrup inter-changeable? Can I substitute regular refined (table) sugar equally for honey or maple syrup?

    1. Assistant to 100 Days (Amy)

      Hi Cora. You can sub honey and maple syrup pretty much interchangeably though their consistencies are a bit different. You cannot, however, substitute a dry ingredient like sugar 1:1. ~Amy

  55. This is now my favorite muffin recipe!!! I ran out of honey before I filled my half a cup, I added a little maple syrup (still did not fill the 1/2 cup tho) and they still turned out great!

    1. Assistant to 100 Days (Amy)

      Hello Viviana. We’ve not tried that but I would think that it might not work out well because of the difference in moisture content. ~Amy

  56. I figured Amy. I am new to baking. They were wonderful! This is my favorite website on the internet! My family loves the food. I love the tips and ideas.

  57. 5 stars
    I made these last week and my 7 year old refused to try them because “he hates cooked carrots.” He finally broke down and tasted them and now LOVES them. We will definitely be including these in our school lunch rotation. Thanks!

  58. These were so soft and moist! I usually have to reduce the amount of sugar or sweetener used in a recipe because our family doesn’t like things too sweet, but these turned out to be just perfect without any adjustments. I didn’t have any apple sauce on hand, so I pureed one apple instead. I also increased the carrots to 1 and 1/2 cups and sprinkled walnuts on top. They turned out great! Thank you for sharing this wonderful recipe!

    1. Assistant to 100 Days (Amy)

      Hi Sarah. We can rarely answer recipe questions in real time. Did it turn out okay. My guess would be yes. ;)

  59. I just made these. I used about 1/4 cup coconut oil and 1/4 cup applesauce in place of the butter (my 11 month old is MSPI) and maple syrup instead of honey and they are amazing! I ate 2 already. I am planning on making these for my son’s birthday cake. I can’t wait for him to try them in the morning (if I don’t eat them all!) :)

  60. Hello,

    I would like to try making these muffins but before I do I would REALLY LIKE THE *NUTRITION INFORMATION* is it posted somewhere and I’m just not finding it?

    Thank you :)

    1. Assistant to 100 Days (Amy)

      Hi Ashley. We do not provide nutrition information. Our focus is on helping people get off the processed stuff and eat real whole foods, not so much on numbers. There are online tools that will calculate all those details for you, however. ~Amy

  61. 5 stars
    I love these! We add raisins, and when all my littles get enough teeth, we’ll probably add pecans. My 3yo is very much about routines (aren’t they all) and I was so surprised that he loved them in place of his normal pb&j waffles. I also add a little cloves.

  62. These are so good! My 3 year old and 21 month old loved them! I was out of butter so I used coconut oil and they are so good. They were heavy weight wise but light and fluffy, and so filling. I think I will add even more finely shredded veggies next time! Thank you!

  63. I loved these being fluffy but they just crumbled in my toddlers’ hands and they didn’t like that so much. Is there anyway to make these a little more dense?

  64. Can I use white whole wheat flour? In general, for your recipes can I make that substitution if needed (based on what I have on hand).

  65. I just made this with the leftover pulp from a carrot/apple juice we made. I also substituted a very ripe banana for the applesauce because I wanted to use it up, everything else was the same. The muffins came out sooo good and moist. My kids love them. I will definitely make these again to use juicing pulp.

  66. 5 stars
    Made these today with my 2.5 year old son. He is a fairly picky eater, but he inhaled three of these muffins before they could even cool. I loved them too. Will definitely make them again!

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