Healthy Carrot Cake Muffins (Gluten-Free)

Last updated March 19, 2026 By Kelly Nardo | 1 Comment
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Healthy carrot cake muffins with raisins, walnuts, applesauce, maple syrup, and warming spices, and topped with greek yogurt frosting! They are easy to make, lightly sweetened, perfectly moist, and so delicious! Enjoy them for breakfast, a healthy snack, or an option for meal prep.
Prep: 10 minutes
Cook: 25 minutes
Cool Time 15 minutes
Total Time: 50 minutes
Servings 9 muffins
5 from 1 vote

Cake for breakfast! Specifically, these healthy carrot cake muffins! They are full of fresh carrots, warm spices, moist, and have a great texture thanks to the added raisins and nuts. And of course are absolutely delicious!

Carrot cake muffins topped with greek yogurt frosting and cinnamon on a wire cooling rack. There is also a bowl of icing on the rack.

While I am a huge fan of cream cheese frosting, to lighten these carrot muffins up, I went with a greek yogurt frosting, which is just greek yogurt, maple syrup, and vanilla. It’s the perfect topping for these muffins. They are just as delicious without any icing if you want to skip it, though!

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Enjoy them for a healthy breakfast, dessert, or make a batch for meal prep to have some healthy snacks on hand for the week. They are the perfect addition to your Easter menu as well!

Why you’ll love this carrot cake muffin recipe

  • made from simple ingredients and so delicious!
  • lightly sweetened – we are using just maple syrup and applesauce.
  • gluten-free – but I promise no one would even know!
A wire cooling rack with carrots cake muffins spread across it. One of the muffins is broken open. Also on the rack is a bowl of raisins, bowl of walnuts, and an orange kitchen towel.

Is carrot cake healthy?

Cake is usually prepared with a decent amount of sugar and fat and can be calorie-dense. Carrot cake does have fresh carrots, which are full of carotenoids (antioxidants high in cancer-fighting properties), vitamin A, calcium, potassium, and fiber, but it is still cake. Of course, all foods can be enjoyed in moderation.

When making it at home, you have full control over the quality and quantity of the ingredients. Our version is lightly sweetened with maple syrup and not full of sugar and fat.

Ingredients

  • 1:1 gluten-free flour – I used Bob’s Red Mill.
  • cinnamon
  • ground ginger
  • nutmeg
  • baking soda
  • baking powder
  • salt
  • unsweetened applesauce – this helps add some natural sweetness and keep them moist. I promise you can’t taste it though!
  • egg
  • milk – any kind will work.
  • maple syrup – for a touch of sweetness.
  • vanilla extract
  • finely shredded carrots
  • raisins – they add a little chewiness and natural sweetness. You can leave them out if you don’t like them.
  • walnuts – for a little crunch. Again, you can leave them out if you don’t like them.
  • greek yogurt frosting – optional, but makes them extra delicious!
A bowl of applesauce, a small bowl of vanilla extract, a plate of a few piles of different spices, a small bowl of baking powder, a measuring cup of maple syrup, a bowl of chopped walnuts, a small bowl of salt, a bowl of grated carrots, a bowl of greek yogurt, a cup of milk, a bowl of raisins, a bowl with a cracked egg in it, a bowl with flour and a flour scoop in it, and a small bowl of baking soda on a tan counter.

How to make healthy carrot cake muffins

  1. Preheat oven to 350 degrees Fahrenheit. Line a muffin pan with 9 nonstick liners.
  2. Mix your dry ingredients. Add your flour, cinnamon, ginger, nutmeg, baking soda, baking powder, and salt to a medium bowl and whisk to combine.
  3. Mix your wet ingredients. In a separate medium-large bowl, add your applesauce, egg, milk,  maple syrup, and vanilla extract and mix well to combine. Add carrots and stir to combine.
  4. Combine batter. Add your dry mixture, raisins, and walnuts to your wet mixture and mix with a spatula until just combined. Do not overmix the batter.
  5. Bake. Using a cookie scoop (about 2 1/2 tablespoons), distribute the muffin batter evenly among the prepared muffin cups. Bake for 25-30 minutes. You can check doneness by inserting a toothpick in the center. It should come out clean with a few moist crumbs. Let cool.
  6. Optional – while the muffins bake, make your frosting. Place in the fridge to let the frosting chill until the carrot cake muffins are cool.
  7. Ice muffins. Once the muffins are cooled, add about a heaping tablespoon of frosting to each muffin and evenly spread it out. I like to sprinkle a little cinnamon on top.
  8. Enjoy!

How to grate carrots

To grate your carrots, use a box grater with small to medium-sized holes. You don’t want your carrot pieces too large, but also not too small that they disappear. I suggest peeling them before grating, as the outside skin can be a little bitter. You can also shred them in a food processor.

Carrot cake greek yogurt frosting

Instead of your classic cream cheese frosting, we are using a greek yogurt frosting. It’s lighter yet still full of flavor and also packs a little protein. You will need:

  • Greek yogurt – I like using Icelandic skyr as it’s super thick. Use full-fat for the best flavor!
  • vanilla extract
  • maple syrup

Simply mix together the ingredients until combined and adjust according to taste. If you prefer a cream cheese frosting, follow this recipe.

Storage

  • fridge – first, let the muffins cool completely. Add to an airtight container and store in the refrigerator for up to a week.
  • freezer – if freezing, I suggest not icing them as the icing consistency will change. Let cool completely and place muffins on a large plate or baking sheet. Place in the freezer and let freeze for 2 hours or until hardened. This will help ensure they freeze individually and won’t stick together. Transfer to a large bag (we love these reusable silicone bags) and freeze for up to 3 months. You can also wrap each one individually after they have cooled. Thaw by placing them in the refrigerator and then letting them come to room temperature. Warm up the microwave if desired.
Healthy carrot cake muffins in white silicone liners in a muffin tin after they were baked.

Substitutions

  • 1:1 gluten-free flour – all-purpose flour will work instead, but the recipe will no longer be gluten-free.
  • applesauce – you can swap out a ripe banana instead. Simply mash it before adding your remaining wet ingredients.
  • egg – I haven’t tried any substitutes, but you could try a flax egg. I am not sure if it will work.
  • milk – dairy or non-dairy will work.
  • maple syrup – honey will work instead.
  • vanilla extract – vanilla bean paste will work the same.
  • raisins – leave them off if you don’t like them.
  • walnuts – pecans or almonds will work instead.
  • greek yogurt frosting – use dairy-free yogurt if needed. You can also swap out your favorite frosting recipe if you prefer.

If you love quick and easy meals and want to learn how to build a balanced plate, check out our FREE How to Build a Balanced Plate Guide!

Healthy carrot cake muffins with greek yogurt frosting on a wire cooling rack. The one in front has a bite taken out of it.
Healthy carrot cake muffins with greek yogurt frosting on a wire cooling rack. The one in front has a bite taken out of it.
5 from 1 vote

Healthy Carrot Cake Muffins

Author: Kelly Nardo
Healthy carrot cake muffins with raisins, walnuts, applesauce, maple syrup, and warming spices, and topped with greek yogurt frosting! They are easy to make, lightly sweetened, perfectly moist, and so delicious! Enjoy them for breakfast, a healthy snack, or an option for meal prep.
Print Recipe Pin Recipe
Course: Breakfast, Snack
Calories: 163kcal
Protein: 3.1g
Carbs: 27.6g
Fat: 5g
Prep Time: 10 minutes
Cook Time: 25 minutes
Cool Time: 15 minutes
Total Time: 50 minutes
Servings: 9 muffins

equipment

ingredients

instructions

  • Preheat oven to 350 degrees Fahrenheit. Line a muffin tin with 9 nonstick paper muffin liners, reusable silicone liners, or grease the muffin wells.
  • Mix your dry ingredients. Add your flour, cinnamon, ginger, nutmeg, baking soda, baking powder, and salt to a medium bowl and whisk to combine.
  • Mix your wet ingredients. In a separate medium-large bowl, add your applesauce, egg, milk,  maple syrup, and vanilla extract and mix well to combine. Add carrots and stir to combine.
  • Combine batter. Add your dry mixture, raisins, and walnuts to your wet mixture and mix with a spatula until just combined. Do not overmix the batter.
  • Bake. Using a cookie scoop (about 2 1/2 tablespoons), distribute the muffin batter evenly among the prepared muffin cups. Bake for 25-30 minutes. You can check doneness by inserting a toothpick in the center. It should come out clean with a few moist crumbs. Let cool.
  • Optional – while the muffins bake, make your frosting. Place in the fridge to let the frosting chill until the carrot cake muffins are cool.
  • Ice muffins. Once the muffins are cooled, add about a heaping tablespoon of frosting to each muffin and evenly spread it out. I like to sprinkle a little cinnamon on top.
  • Enjoy!

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nutrition

Nutrition Facts
Healthy Carrot Cake Muffins
Amount Per Serving (1 muffin (without icing))
Calories 163 Calories from Fat 45
% Daily Value*
Fat 5g8%
Saturated Fat 0.8g5%
Polyunsaturated Fat 2.9g
Monounsaturated Fat 0.8g
Cholesterol 22mg7%
Sodium 289mg13%
Potassium 150mg4%
Carbohydrates 27.6g9%
Fiber 1.8g8%
Sugar 10.8g12%
Protein 3.1g6%
Vitamin A 805IU16%
Vitamin C 1mg1%
Calcium 73mg7%
Iron 0.7mg4%
* Percent Daily Values are based on a 2000 calorie diet.
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Recipe by Kelly Nardo, Eat the Gains | Photography by Sierra Inn

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5 from 1 vote

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