Whole Wheat Carrot Applesauce Muffins

150 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?)!
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carrot applesauce muffins

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These carrot applesauce muffins are made with whole wheat flour and other real food ingredients. This recipe is a huge hit with the kids; they taste just like carrot cake!

Featured Comment

This 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 (not recommended younger than 1 year old), then 100% pure maple syrup would work just fine as a substitute.

Are Muffins Made with Carrot and Apple Healthy?

Healthy can mean different things to different people. Since these carrot muffins are made with whole wheat flour and honey instead of sugar, they’re definitely a lot healthier than most muffin recipes.

Feel free to make your own applesauce! Read up on the types of apples.

The carrot and applesauce add a sweet flavor, but they’re also nutritious, too! These Sweet Potato Muffins are another healthy option.

Why Carrot is Great in Muffins

If you’re a fan of carrot cake you probably already know how delicious carrots can be as a baking ingredient. Naturally sweet, carrots help soften (and sweeten) anything they’re baked into. And, while it’s not the same as a complete healthy meal, it’s always nice when you can add a few extra veggies into what we eat.

How to Make This Homemade Carrot Muffin Recipe

  1. First, preheat the oven to 350 degrees F and line your muffin pans.
  2. While the oven heats, whisk together the dry ingredients (whole wheat flour, baking soda, cinnamon, ginger, and salt).
  3. In a separate bowl (I use an electric mixer), beat the softened butter, honey, egg, and vanilla on medium speed.
  4. Set mixer to low, then slowly beat in the flour mixture.
  5. Fold in the applesauce and shredded carrots.
  6. Divide batter evenly among 12 muffin cups a bake for 22-24 minutes, or until a toothpick pressed into the center comes out clean.

Can You Freeze These Muffins?

Absolutely! All my muffin recipes freeze well, including these carrot muffins. To freeze, simply cool completely then place in an airtight container. Muffins keep in the freezer for up to three months.

To thaw, warm up on the counter overnight or microwave for about 30 to 60 seconds. You can also put frozen muffins right into kids’ lunches and they should be thawed by the time they’re ready to eat!

Tips for Shredding Carrots

  • You’ll need to peel your carrots before shredding them; carrot peels can sometimes make carrot muffins taste bitter.
  • The easiest way to shred carrots is with a box style cheese grater, preferably using the smaller size holes.
  • Some food processors can also shred carrots.

Can This Recipe Be Doubled?

Yes, but sometimes muffins can bake differently when the recipe is doubled, depending on your oven. If you run into issues, I’d recommend baking one tray of muffins at a time, which is better for even baking anyway!

Will This Recipe Work for Mini Muffins or a Loaf?

You can definitely make muffin muffins instead of full-sized ones, just adjust the cooking time to about 12-14 minutes so they don’t overbake.

We haven’t had the chance to try this recipe in a loaf pan or as a cake yet, but if you do let us know how it turns out in the comments!

Make Carrot Cake Muffins for Dessert

This recipe already uses carrot cake spices and ingredients—they’re basically carrot cake muffins! But if you want to turn these muffins into an easy real food dessert, simply add frosting.

Carrot cake is normally topped with cream cheese frosting, but that’s loaded with powdered sugar. Instead, make a cream cheese glaze by mixing 8 oz of softened cream cheese, ¼ cup of honey, and ½ teaspoon of vanilla.

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Recipe Rating

  1. 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.

  2. 5 stars
    We love these!!!!! How many muffins are a serving? I am meal prepping so I want to calculate caloric intake. Thank you

  3. 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.

  4. 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!

  5. 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

  6. 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!

  7. 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!

  8. 5 stars
    Have made these multiple times and they are always a huge hit!! I typically have to make more than one batch.

  9. 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!

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

  11. 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.

  12. 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!

  13. 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?

  14. 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?

  15. 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!!!

  16. 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.

  17. 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)

  18. 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!

  19. 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.

  20. 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.

  21. 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

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