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
    Love these muffins! My new favorite for this Fall & Winter.
    I kept the recipe the same as Lisa’s with 1 extra ingredient though… Chopped Dates, yummy!
    I chopped up 6 Medjool pitted Dates that I had in the freezer. I added the Dates in when I folded in the Applesauce and grated Carrots. It was a terrific addition and flavor compliment to the muffins!
    Thank you Lisa for this delicious recipe!

  2. 5 stars
    Soooo good! I was looking for something to do with extra carrots and applesauce that needed to be used up and this recipe popped into my FB feed. I had all of the ingredients on hand and this was super easy to make. I wanted them to have more of a carrot cake flavor so I tripled the cinnamon and ginger and added some ground clove and nutmeg. I also added some golden carrots and walnut pieces. I made two batches but I don’t think the extra batch will be in the freezer for long because I love these so much.

  3. My muffins didn’t rise… at all. They also took almost an hour to thoroughly cook. The taste was really good, though… but they were very dense. I don’t think I over mixed… but could that be the culprit?

    1. We always recommend you have fresh baking soda and other ingredients for the best results. And of course, making sure you fold in the applesauce and not over mix it. Altitude can sometimes play a role in baked goods not rising, as well. – Nicole

  4. Going to try these this week! Would you alter the recipe at all if using your Easy Peasy Applesauce? It has a little honey already so I wasn’t sure if that would change things at all. Thanks so much!

    1. While we haven’t tested with that applesauce, you could reduce the amount of added honey since it already has some. Please let us know how they turn out and what you decided to do! – Nicole

  5. I need to adjust recipes for a diabetic, so I’m wondering if it is better to replace the honey with liquid stevia or powdered stevia/erythritol ? Thanks

  6. What cookbook is this in? I keep finding myself printing recipes and then finding the same recipe in one of your cookbooks (I love them all!). I’m just trying to save the planet one unnecessarily printed recipe at a time.

  7. 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.

  8. 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!

    1. I followed the recipe and my muffins didn’t rise… at all. I don’t think I over mixed it… but has this been an issue for anyone else?