In the Great Muffin Debate—in which one side claims that muffins should actually be healthy and the other side insists they should actually be cake—these Carrot Cake Muffins will appease you.

Moist Carrot Cake Muffins with Cream Cheese Frosting

To the devotees on the healthy muffin recipe side (a.k.a. the right side—I’m sorry, did I give myself away too quickly there?), these muffins are made of wholesome ingredients, and you’ll feel great starting your day with a warm plate of them.

To those on the side of muffins-as-cake, this recipe lives up to its name, Carrot CAKE Muffins. Like these Zucchini Carrot Muffins, they’re moist and just the right amount of sweet, and if the tender crumb of the muffins doesn’t convince you, then the cream cheese frosting on top will.

Healthy Carrot Cake Muffins with cream cheese frosting

Carrot Cake Muffins—A Recipe That’s Healthy and Delicious

On the healthy muffin front, here’s what you’ll love about these Carrot Cake Muffins:

  • Whole Grains. Mild whole wheat flour is my weapon of choice; whole wheat pastry flour works nicely too.
  • Refined Sugar Free. Honey is the only sweetener.
  • No Butter or Oil. Instead, I baked these moist Carrot Cake Muffins with applesauce and almond butter.
  • Loads of Carrots. Two full cups! Go back for seconds and thirds.
  • Healthy Mix-Ins. Classic carrot cake additions like walnuts and golden raisins make these muffins better for you and better tasting too.

A bowl of ingredients for Carrot Cake Muffins

NOW, before you get the idea I’m serving you a healthy carrot cake muffin that tastes overtly, well, healthy, please know that I will never suggest a recipe that sacrifices taste.

Life is too short for dry, crumbly, bland muffins. That’s why, like my Healthy Blueberry Muffins, Applesauce Muffins, Healthy Banana Muffins, and all of these healthy muffin recipes, today’s Carrot Cake Muffins are moist and sweet, and you’ll look forward to waking up to them in the morning.

  • Spices. Cinnamon, nutmeg, and cloves give carrot cake its signature taste, so I included plenty of them here too!
  • Cream Cheese Frosting. I simply could not, out of good faith and respect to carrot cake, give you a Carrot Cake Muffin recipe without cream cheese. Even if you aren’t usually a frosted muffin fan (I’m not), the cream cheese frosting makes these muffins truly special.
  • Mega Moisture. Carrots, applesauce, and almond butter combined give these muffins a tender interior. They’re still sturdy (I like my carrot cake with a bit of a thud) but are not dry by any means.

A pan of six Carrot Cake Muffins

Tips for Faster Carrot Cake Muffin-Making

I streamlined this Carrot Cake Muffin recipe to make it as easy as possible. You don’t need a mixer to make them; just two bowls and a whisk.

The only tedious part is grating the carrots, a step I managed to trim down to about 10 seconds thanks to the shredder blade on my food processor.

Remember that contraption that came in the box with yours (it probably looks something like this)? You likely have it sitting in the back of your pantry right now.

Food processor bowl full of grated carrots

I know washing a food processor is the worst, but for grating large numbers of veggies like carrots (along with zucchini for these Healthy Zucchini Muffins and carrots and apples for these Apple Carrot Muffins), it is well worth the effort.

A few of you watched the carrot shredding when I shared it on Instagram and are believers too!

Carrot Cake Muffins with cream cheese frosting

Recipe Variations

  • Vegan Carrot Cake Muffins. I haven’t yet tested this recipe with flax eggs, but I think that swap would be worth experimenting on your own (and if you try, I’d love to hear how it goes). Use maple syrup for honey and a tofu or other dairy-free cream cheese substitute for the frosting.
  • Gluten Free Carrot Cake Muffins. Swap the all purpose and whole wheat flour for a gluten free 1:1 baking flour like this one.
  • Mix-Ins. Not into nuts or golden raisins? You can simply omit them or add a different mix-in like toasted sunflower seeds and/or dried cranberries.

Recommended Tools to Make Healthy Carrot Cake Muffins 

Looking for the Best Ever Carrot Cake Recipe?

  • It’s in my upcoming cookbook! Stay tuned for more updates—it will be here in 2020. I’ll be sharing all of the details about its release here on my site and on Instagram.
  • If you’d like to receive email updates so that you don’t miss any details, you can sign up here. It’s totally free, and I’ll send you an e-cookbook as a thank-you.

While we wait for my cookbook, these Carrot Cake Muffins are here to appease your carrot cake cravings.

These Carrot Cake Muffins should be stored in the fridge and taste even better on Day 2, so they’re an ideal make-ahead option for a special brunch (Mother’s Day perhaps?).

And on any day, they’re a wholesome breakfast that will start your morning with pizzazz. I hope you love them too!

Moist Carrot Cake frosting with Cream Cheese Frosting

Carrot Cake Muffins

5 from 5 votes
Moist Carrot Cake Muffins with Cream Cheese Frosting. Tender, healthy muffins that taste like your favorite carrot cake! Made with applesauce, whole grain, and refined sugar free.

Prep: 15 mins
Cook: 15 mins
Total: 1 hr

Servings: 12 muffins


For the Muffins:

  • 1/2 cup raw pecans or walnuts
  • 1 1/3 cups white whole wheat flour or whole wheat pastry flour*
  • 2/3 cup all-purpose flour
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1 1/2 teaspoons ground cinnamon
  • 1/4 teaspoon ground nutmeg
  • 1/4 teaspoon ground cloves
  • 1/4 teaspoon kosher salt
  • 2 cups packed coarsely grated carrots from about 9 ounces or 4 medium carrots
  • 1/3 cup golden raisins
  • 1/4 cup creamy almond butter or cashew butter the drippy, natural kind**
  • 1/4 cup unsweetened applesauce
  • 1/3 cup honey
  • 2 large eggs
  • 1/2 cup plus 2 tablespoons unsweetened almond milk or milk of choice
  • 1 teaspoon pure vanilla extract

For the Cream Cheese Frosting:

  • 4 ounces reduced-fat cream cheese softened to room temperature
  • 3/4 cup powdered sugar sifted if lumpy
  • 1/2 teaspoon pure vanilla extract
  • 1/2 teaspoon finely grated lemon or orange zest optional


  • Preheat the oven to 350 degrees F. Spread the nuts in a single layer on an ungreased baking sheet. Toast them in the oven until crisp and fragrant, about 8 to 10 minutes. Set a timer and do not walk away from the nuts during the last few minutes of baking (this is when nuts love to burn). Transfer to a cutting board and roughly chop. Set aside 1/4 cup for the muffin batter. Finely chop the remaining nuts and save for sprinkling on top.
  • Increase the oven heat to 400 degrees F. In a large mixing bowl, stir together the white whole wheat flour, all-purpose flour, baking powder, baking soda, cinnamon, nutmeg, cloves, and salt. Add the carrots, golden raisins, and reserved 1/4 cup chopped nuts. With a spoon or flexible spatula, gently fold to combine.
  • In a medium mixing bowl, whisk together the almond butter, applesauce, and honey until smooth. Whisk in the eggs, milk, and vanilla. Add to the carrot and flour mixture. With a wooden spoon or spatula, fold and stir very gently by hand, stopping as soon as the flour disappears.
  • Coat a standard 12-cup muffin pan with nonstick spray or line with paper liners. Fill each about three-quarters of the way with batter. (If you have some extra batter, resist the urge to overfill the muffin cups; you can bake the extra as soon as the first batch is out). Bake the muffins for 14 to 16 minutes, or until the muffins are domed, light golden on top, and a toothpick inserted into the center of each comes out clean. Place the pan on a cooling rack and let the muffins cool in the pan for 5 minutes, then gently remove them from the pan and place them on the rack to cool completely (do not leave the muffins in the pan for longer or they can become too soggy as they start to steam).
  • For the cream cheese frosting: In a medium mixing bowl, place the cream cheese, powdered sugar, vanilla extract, and lemon zest (if using). With an electric mixer on low speed, beat until the powdered sugar begins to incorporate, then increase the heat to medium and continue to beat until smooth and creamy. Frost the cooled muffins and sprinkle with the remaining finely chopped walnuts.


  • *You can use regular whole wheat flour, but the wheat will have a more pronounced taste than white whole wheat flour or whole wheat pastry flour.
  • **You can use peanut butter as well, though the flavor will be different. I recommend this recipe with a drippy, natural-style nut butter, as that will give the muffins the right consistency, though a shelf-stable almond butter I tested still yielded good results.
  • Store leftovers in the refrigerator for up to 4 days (they taste even better on Day 2). Freeze according to my guide for how to store muffins and other quick breads.


Serving: 1muffinCalories: 244kcalCarbohydrates: 38gProtein: 6gFat: 8gSaturated Fat: 1gCholesterol: 32mgFiber: 3gSugar: 20g

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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  1. I just took these muffins out of the oven! I was happily surprised that I got almost 2 dozen! I love your recipes! Whenever I need a never fail recipe I go to your website first. I love your passion for cooking and my family enjoy your recipes. 5 stars

  2. Hi Erin!

    I’m excited to try these– they sound delicious! Quick question– I only have a mini muffin pan. Would this recipe still work for that? Could I just cut down the baking time?

    Thanks so much! :)

    1. Hi Tanya! I’ve never tried this recipe in a mini muffin pan, so it would be an experiment. I suggest checking them very early and often to make sure they don’t burn. If you decide to try it, I’d love to hear how it goes!

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