Healthy Carrot Cake Muffins

4.75 from 4 votes

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Healthy Carrot Cake Muffins are a nourishing spin on a springtime classic and have all the flavors you love in carrot cake (raisins, nuts, carrots), plus you can get away with having them for breakfast. And that’s just a win-win.

muffins on a metal rack with carrot pieces and raising showing through top.
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Disclosure: This post is sponsored by Bob’s Red Mill. Thank you for supporting the brands that I love and choose to partner with. 

I’m so excited to be working with Bob’s Red Mill today. I’ve been a long-time fan and customer of this employee-owned company. They embody so much of my passion and joy when it comes to eating and feeding people well. It’s an honor to have worked with them this whole year, and I hope you love the recipes I create using their products.

muffins in a blue and white muffin pan with small bowl of shredded carrot, cinnamon sticks, raisins, and a bag of flour on a red and white striped towel.

These Healthy Carrot Cake Muffins check all the boxes for spring pastries. They’re hearty and sweet, but not too sweet, plus they are sneakily nutritious, kind of like Spring oatmeal cookies with M&Ms!

They’ve got all the goodness of classic carrot cake, but you can have them for breakfast! If you’d rather save them for dessert, add a layer of simple cream cheese frosting (recipe below) to turn your muffin into a makeshift cupcake.

muffins on a metal rack with carrot pieces and raising showing through top with small bowl of shredded carrot on a blue and white striped towel.

Why You’ll Love This Recipe

  • Moist, filling, and packed full of your favorite Spring flavors, you’ll surely have several happy bellies at table.
  • A sneaky way to get in some extra nutrition with the carrots, raisins, nuts, and whole wheat flour!
  • These muffins are a great choice for breakfast, snacks, or even dessert.

Recipe Ingredients

I’m partnering with one of my favorite clients for this recipe today! These muffins are made with Bob’s Red Mill whole wheat pastry flour, coconut oil, honey for the sweetness, raisins, nuts, and, of course, carrots.

  • Coconut oil – or use melted butter or another vegetable or nut oil
  • Honey
  • Applesauce – unsweetened to keep the sugar content lower
  • Egg
  • Vanilla extract
  • Bob’s Red Mill Whole Wheat Pastry Flour
  • Baking soda
  • Spices – cinnamon, nutmeg, and ginger
  • Carrots
  • Raisins
  • Nuts – pecans and walnuts are both yummy in carrot cake recipes

See the recipe card below for full information on ingredients and quantities.

muffins in a blue and white muffin pan with small bowl of shredded carrot, cinnamon sticks, raisins, on a red and white striped towel.

How to Make Healthy Carrot Cake Muffins

  1. Combine all wet ingredients in a bowl.
  2. Add flour, baking soda, and spices. Mix well.
  3. Fold in the carrot, raisins, and nuts.
  4. Bake until a toothpick inserted into the center comes out clean.

Recipe FAQs

Can you freeze Healthy Carrot Cake Muffins?

Yes! To freeze, let cool completely, wrap individually in aluminum foil or plastic wrap to maintain their moisture, and place in a plastic bag or airtight container in the freezer. They’ll keep for up to 3 months frozen.

How do you store Healthy Carrot Cake Muffins?

These guys are nice and moist, and you want to be sure you store them in a way to preserve that great texture. Let the muffins cool completely before transferring them to a sealable plastic bag or airtight container. Putting them in the fridge will take away from the flavor, so leave them in a room temperature area. They’ll stay fresh for up to 4 days.

muffins on a metal rack with carrot pieces and raising showing through top with small bowl of shredded carrot on a blue and white striped towel and one muffin opened with butter on top on a white plate.

Expert Tips

  • Have you tried whole wheat pastry flour before? It’s magical! Made from a soft white wheat berry (that’s what the kernel of wheat is called), it has all of the nutrition of whole grain whole wheat flour but yields a lighter and fluffier product than traditional whole wheat. It’s a great choice of flour for muffins, cookies, and other baked goods.
  • These muffins freeze great and will stay fresh covered at room temperature for 3 to 4 days.
  • These healthy muffins are perfect snacks or on-the-go breakfasts, but they can also be served as a healthier dessert choice with the addition of cream cheese frosting. Another delicious—and impressive—healthy-ish dessert is my carrot cake roll. Can you go wrong with a carrot-themed dessert?
muffins in a blue and white muffin pan with small bowl of shredded carrot, cinnamon sticks, raisins, and a bag of flour on a red and white striped towel.

Cream Cheese Frosting for Carrot Cake Muffins

Cream cheese frosting will definitely add more decadence to these muffins and make them more reminiscent of their classic cake cousin. This simple cream cheese frosting recipe will work nicely.

Ingredients:

  • 8 ounces cream cheese, softened
  • 1 cup unsalted butter at room temperature
  • 2 lb powdered sugar, approximately 8 cups
  • ⅛ teaspoon salt
  • 2-4 tablespoons heavy cream

To make:

  1. Cream the cream cheese and butter together until light and fluffy.
  2. Gradually mix in powdered sugar a little at a time. Beat well for a few minutes to ensure a velvety texture.
  3. Add cream to reach a spreadable texture, and beat 3 to 4 minutes.
  4. Spread over the top the cooled muffins.

More Healthy Muffin Recipes to Consider

Healthy Carrot Cake Muffins are a nourishing spin on a springtime classic and have all the flavors you love in carrot cake (raisins, nuts, carrots), plus you can get away with having them for breakfast. And that's just a win-win.
4.75 from 4 votes

Healthy Carrot Cake Muffins

Healthy Carrot Cake Muffins are a nourishing spin on a springtime classic and have all the flavors you love in carrot cake (raisins, nuts, carrots), plus you can get away with having them for breakfast. And that’s just a win-win.
Prep: 15 minutes
Cook: 20 minutes
Total: 35 minutes
Servings: 12 muffins

Ingredients 

  • 2 tablespoons melted coconut oil, or melted butter or oil
  • 1/2 cup honey
  • 1 cup unsweetened applesauce
  • 1 large egg
  • 2 teaspoons vanilla extract
  • 1 1/2 cups Bob's Red Mill Whole Wheat Pastry Flour
  • 1 teaspoon baking soda
  • 1 teaspoon ground cinnamon
  • 1/4 teaspoon ground nutmeg
  • 1/4 teaspoon ground ginger
  • 1/2 teaspoon salt
  • 3/4 cup finely grated carrot
  • 1/2 cup raisins
  • 1/2 cup chopped pecans, or walnuts, if you prefer
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Instructions 

  • Preheat the oven to 350 degrees F. Lightly spray a 12-cup muffin tin with cooking spray.
  • In a large bowl, add the coconut oil, honey, applesauce, egg, and vanilla extract. Stir well to combine.
  • Add the flour, baking soda, cinnamon, nutmeg, and ginger. Stir until just combined.
  • Gently fold in the carrot, raisins, and pecans.
  • Divide the batter evenly among the 12 cups of the muffin tin.
  • Bake for 18 to 24 minutes, or until a toothpick inserted into the center comes out clean.
  • Let the muffins rest in the pan for 5 minutes, and then remove and let them finish cooling on a wire rack.
  • Eat warm or at room temperature. These muffins freeze great and will stay fresh covered at room temperature for 3 to 4 days.

Notes

  • Not a fan of nuts or raisins? Leave them out! But they are SO good in this recipe that I think you should try it.
  • Bob’s Red Mill traditional whole wheat flour (comes in a tan bag) will also work well in this recipe.
  • These muffins freeze great and will stay fresh covered at room temperature for 3 to 4 days.
  • These muffins are yummy served plain or make give them a “dessert” element by adding cream cheese frosting.

Nutrition

Serving: 1 muffin, Calories: 183kcal, Carbohydrates: 31g, Protein: 3g, Fat: 6g, Saturated Fat: 2g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 2g, Trans Fat: 0.002g, Cholesterol: 16mg, Sodium: 203mg, Potassium: 179mg, Fiber: 3g, Sugar: 14g, Vitamin A: 1369IU, Vitamin C: 1mg, Calcium: 19mg, Iron: 1mg
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16 Comments

  1. Iris says:

    Can almond flour be used in this recipe ?

    1. Melissa says:

      I haven’t tried it, I think it would change the texture considerably and they would be quick crumbly.

  2. Brenda says:

    Have you tried this recipe with Bob’s Red Mill gluten free all purpose flour?

    1. Melissa says:

      I haven’t but I have great luck with that flour and it seems to translate really well to things like quick bread and muffins, I’d definitely try it.

  3. averiesherburne@gmail.com says:

    Can i use King Arthur Brand whole wheat flour? or does it have to be pastry flour?

    1. Melissa says:

      The texture is better with the pastry flour but you for sure can use the traditional whole wheat, it’ll work great.

  4. Wendy Katherine Roby says:

    Is it possible to use gluten free four? If so, do you have a recommendation? Thanks!

    1. Melissa says:

      I haven’t tried it with this certain recipe but I do have a lot of luck using GF baking blends, ones that say 1:1 baking blend (I’ve used Bob’s Red Mill baking blend and a Grandpa’s Kitchen baking blend in the past for other recipes and I generally have good luck with them). I’d try it!

  5. Paula Hansen says:

    4 stars
    Nutrition Information, please, on this recipe. ( Nevermind, I found it: 187 calories, versus the 245 calories in the frosted carrot cake muffins that I made last week. Those doubled as my hubby’s birthday cake, though, so that’s okay! I’ll try these, next!)

  6. Jamie says:

    5 stars
    Made these and LOVED them! I was craving carrot cake but was too lazy to make it and these muffins hit the spot! I even froze some and just ate those and they were just as good!

  7. Heather Lewis says:

    5 stars
    These are so moist and delicious. A great time saver in the morning since they freeze and microwave well.

    1. Melissa says:

      I love hearing this!

  8. DaNae says:

    My kids love muffins for breakfast-they’d gobble these up!! Can’t wait to try.

    1. Melissa says:

      They’re a hit for sure. I’d love to hear what your kids think!

  9. Mary Shoaf says:

    5 stars
    I can’t wait to try these. My kids love a good muffin. This seems like a perfect addition. Plus I love the idea of freezing some for future school mornings.

    1. Melissa says:

      You got the idea perfectly! Healthy, kid friendly, and easy to make ahead… I aim to please 🙂 ENJOY!