Healthy muffins! That taste like carrot cake! Oh, I think these healthy carrot cake muffins might just be a dream come true.

Truth be told, carrot cake gets me every single time. I fell in love with it a few years ago and my craving for cake has quadrupled since then. I can’t get over the spices, flavor, and that thick-n-creamy cream cheese frosting that pairs so wonderfully with the cake. I’m not sure it gets better. By the way, if you haven’t tried my grain free healthy carrot cake recipe, DO IT!

But wait, it does. Because now you can officially have carrot cake for breakfast in muffin form. I know, it’s probably not quite the same but my goodness does it crush a carrot cake craving like no other.

What makes these carrot cake muffins healthy?

Traditional muffin recipes can be packed with oil or butter and lots of refined sugars. To make these carrot cake muffins healthier, this recipe is made with applesauce and just a bit of olive oil for moisture plus pure maple syrup to sweeten them naturally. That’s right, these muffins aren’t baked with any refined sugars (except the glaze if you use it!)

ingredients for carrot cake muffins on a grey board

Everything you need to make carrot cake muffins

Not only are these carrot cake muffins delicious, but they’re also made with nutrient-dense, healthy ingredients compared to a regular slice of carrot cake. Naturally sweetened, whole grains and includes both fruits and veggies, making them the perfect brunch treat or snack for both kids & adults. Here’s what you need:

  • Flour: I like to use white whole wheat flour because it has the same nutritional benefits as whole wheat flour, but are much lighter in flavor and texture. You can usually find it at your local grocer. If you can’t, try looking for whole wheat pastry flour.
  • Pure maple syrup: I prefer maple syrup but honey would also do the trick.
  • Unsweetened applesauce: I love baking with applesauce because it naturally sweetens the recipe, adds fiber and vitamins and provides moisture to give these muffins a nice texture. Even though I use a few tablespoons of healthy oil in this recipe, most of the healthy fats come from walnuts or pecans.
  • Milk: feel free to use any milk you’d like! I love using vanilla almond milk or coconut milk for a little extra flavor in the muffins. To keep these dairy free, use a dairy free milk.
  • Eggs: you’ll just need one to help these carrot cake muffins stay together.
  • Shredded carrots: you’ll need to shred about 2-3 medium carrots, but make sure to measure 1 cup full total. If you’re feeling like you want more, you can use 1 1/2 cups.
  • Cozy spices: cinnamon & nutmeg add a cozy flavor to these healthy carrot cake muffins and gives them that carrot cake flavor goodness.
  • For the glaze: cream cheese, powdered sugarvanilla and a splash of almond milk.

mixing batter for healthy carrot cake muffins

Simple ingredient swaps

Out of a few ingredients? Here’s what I can suggest for substitutions:

  • Swap the applesauce. If you’re out of applesauce you can actually use 1 ripe mashed banana instead.
  • Choose the oil. Melted and cooled coconut oil, olive oil and avocado oil will all work well in the recipe. Or choose an oil like walnut or hazelnut oil. Butter also works great — totally up to you!
  • Milk of choice. I like to use almond or coconut milk in this recipe, but feel free to use any milk you’d like.

Can I make them gluten free?

I haven’t tested these carrot cake muffins with a gluten free flour, but I think chickpea flour or an all purpose gluten free flour should work well!

unbaked healthy carrot cake muffins in a muffin tin

How to make vegan carrot cake muffins

Yes, these healthy carrot cake muffins should work well with a vegan substitute! Simply replace the egg with a flax egg. Learn how to make a flax egg here! Remember to also leave off cream cheese frosting (or use a dairy free cream cheese) and instead sprinkle tops with cinnamon and coarse sugar.

Have fun with mix-ins

Try adding shredded coconut, raisins or even fresh pineapple to these carrot cake muffins! Everyone prefers their carrot cake differently, so feel free to add them or enjoy the muffins as-is.

healthy carrot cake muffins in a muffin tin

Tips for the best carrot cake muffins

  • Follow the recipe. The best way to ensure the success of these healthy carrot cake muffins is to follow the recipe and use the exact ingredients as written (unless I note specific substitutes).
  • Use finely shredded carrots. Shred those babies nice and thin so that they mix well in the batter.
  • Do not overmix the batter. If you overmix batter you’ll end up with dense and gummy carrot cake muffins instead of fluffy and soft ones.
  • Use fresh baking soda. If your baking soda is older than 3 months, I suggest grabbing a new one for best baking results.

Looking for a carrot cake bread?

I think these healthy carrot cake muffins can be made into a bread, too! Simply pour the batter into an 8×4 inch loaf pan greased and lined with parchment paper. Bake for 40-55 minutes until a toothpick comes out clean.

Alternatively, try my famous carrot cake banana bread for a wonderful option.

healthy carrot cake muffins with cream cheese glaze on a wooden board

How to store carrot cake muffins

  1. In the fridge: store these carrot cake muffins on the counter in an airtight container for a day, then transfer them to the fridge for up to 4-5 days. The muffins really do get better after sitting in an airtight container for a day; they sweeten up a bit and get super soft. Served with a big glass of almond milk!
  2. Freezer-friendly carrot cake muffins: Feel free to freeze these babies for later! Allow them to cool completely after baking, then place them in an airtight container or reusable bag and freeze for up to 3 months. When you’re ready to eat them, you can microwave them for 45 seconds-1 minute or until warm. I suggest freezing them without the the glaze and simply adding the glaze when you’re ready to enjoy them.

carrot cake muffin with a bite taken out

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I hope you love these healthy carrot cake muffins! If you make them I’d love for you to leave a comment and a rating letting me know how you liked them. I greatly appreciate it – xoxo!

Recipe by: Evi Madison // SRCooking | Photography by: Eat Love Eats

Originally published on Feb 12, 2015, republished on April 4th, 2020, updated with new photos and republished on March 30th, 2021, and republished on April 8th, 2022.