Healthy Carrot Cake Muffins with Cream Cheese Glaze

Healthy carrot cake muffins packed with carrots, coconut, raisins and nuts. These deliciously moist carrot cake muffins are naturally sweetened with pure maple syrup and applesauce. Top them with a light cream cheese glaze for a delicious snack or healthy treat!

Prep Time
10 mins
Cook Time
20 mins
Total Time
30 mins

Healthy muffins! That taste like carrot cake! Oh, I think this 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.

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.

In fact, I’ve been wanting to tell you about these for a few weeks; believe me everyone I’ve been around me has had their fair share of muffins as I tried time and time again to perfect the recipe. Basically shoving muffins down everyone’s throat. Pleasant, right?

Healthy carrot cake muffins on a vintage tray

Ingredients in healthy carrot cake muffins:

  • White whole wheat flour (or whole wheat pastry flour): Same nutritional benefits as whole wheat flour, but 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. To make them gluten free you can try using chickpea flour or an all purpose gluten free flour. I have not tested it, but think it should work well!
  • Pure maple syrup: I prefer maple syrup to honey after reading this interesting article comparing the two.
  • Unsweetened applesauce: I love baking with applesauce because it gives baked goods a nice texture without having to use as much oil. Even though I use a few tablespoons of healthy oil in this recipe, I didn’t want it to be packed with fat. The other healthy fats come from walnuts/pecans.
  • Unsweetened almond milk: feel free to use any milk you’d like! I love using vanilla almond milk for a little extra flavor in the muffins.
  • Eggs: you’ll just need one to help these carrot cake muffins stay together. I haven’t tried using a flax egg, but I suspect it will work well. Let me know if you try it in the comments!
  • Shredded carrots: you’ll need to shred about 2-3 medium carrots, but make sure to measure 1 cup full total.
  • Cozy spices: cinnamon & nutmeg add a cozy flavor to these healthy carrot cake muffins and gives them that carrot cake flavor goodness.
  • Optional add-ins: Try adding shredded coconut, raisins or pineapple to these muffins. Everyone prefers their carrot cake differently, so feel free to add them or enjoy the muffins as-is.
  • For the glaze: cream cheese, powdered sugarvanilla and a splash of almond milk.

sprinkling coconut on a tray of healthy carrot cake muffins

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 I used applesauce and just a bit of olive oil for moisture and pure maple syrup for a natural sweetness. That’s right, these muffins aren’t baked with any refined sugars!

Obviously I didn’t include the cream cheese glaze as healthy, but it’s really quite delicious on top of the muffins. Plus it’s only a tiny amount. If you want though, you could leave off and enjoy them as is. You can also use my paleo powdered sugar recipe to keep these completely refined sugar-free!

Healthy carrot cake muffins in a baking tray next to a carton of Almond Breeze almondmilk

How to store healthy 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.

Healthy carrot cake muffins next to a dish of toasted coconut flakes

More carrot cake recipes you’ll love

Healthier Carrot Cake Banana Bread with Cinnamon Cream Cheese Frosting

Carrot Cake Baked Oatmeal Cups

Carrot Cake Smoothie

Healthy Carrot Cake Cookies (made with coconut oil + dairy free!)

The Best Healthy Carrot Cake You’ll Ever Eat (gluten free & paleo-friendly!)

See how to make the carrot cake muffins:

I hope you love these delicious, 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!

Healthy Carrot Cake Muffins with Cream Cheese Glaze

4.86 from 14 votes
Course Breakfast, Dessert, Healthy, Muffins, Snack
Cuisine American
Keyword healthy carrot cake muffins, moist carrot cake muffins
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Serves 12

Healthy carrot cake muffins packed with carrots, coconut, raisins and nuts. These deliciously moist carrot cake muffins are naturally sweetened with pure maple syrup and applesauce. Top them with a light cream cheese glaze for a delicious snack or healthy treat!


  • 1 1/2 cups whole wheat pastry flour
  • 1 teaspoon baking soda
  • 1/4 teaspoon salt
  • 1 1/2 teaspoons cinnamon
  • 1/4 teaspoon nutmeg
  • 1 cup finely shredded carrots (about 2-3 carrots)
  • 1/2 cup pure maple syrup
  • 1 tablespoon olive oil
  • 1/3 cup natural unsweetened applesauce
  • 1 egg, slightly beaten
  • 2 teaspoons vanilla extract
  • 1/2 cup almond milk
  • 1/2 cup unsweetened shredded coconut flakes (optional and not included in nutrition info)
  • 1/2 cup raisins (optional and not included in nutrition info)
  • 4 oz reduced fat cream cheese, softened
  • 1/4 cup powdered sugar
  • 1/2 teaspoon vanilla extract
  • 1-2 tablespoons almond milk


  1. Preheat oven to 350 degrees F. Line 12-cup muffin pan with liners and spray the inside with nonstick cooking spray to prevent batter from sticking to the liners. You can also omit the liners and generously spray the muffin pan with nonstick cooking spray; I prefer this method.
  2. Next add flour, baking soda, cinnamon, nutmeg and salt to a medium bowl; stir to combine and then set aside.
  3. In a separate large bowl, add carrots, maple syrup, olive oil, applesauce, egg and vanilla. Whisk to combine wet ingredients then slowly stir in almond milk and flour mixture until just combined. 
  4. Fold in coconut flakes and raisins if you'd like. Divide batter evenly between muffins cups or liners. 
  5. Bake for 18-20 minutes or until toothpick inserted into the middle comes out clean. Allow to cool for 10 minutes in pan then transfer muffins to a wire rack to finish cooling.
  6. Once muffins are completely cool, you can make the cream cheese glaze: Place cream cheese in medium microwave safe bowl and microwave on high for 30-45 seconds or until cream cheese is somewhat warm and a little runny. 
  7. Stir gently and add in powdered sugar, vanilla extract and a few tablespoons of milk; stir again until glaze reaches desired consistency; not too runny and not overly thick. 
  8. Dip each muffin top into cream cheese glaze then place back on wire rack. Sprinkle with coconut flakes if desired. Makes 12 muffins.

Recipe Notes

To make vegan: Replace egg with a flax egg by combining 1 tablespoon flaxseed meal and 3 tablespoons of water. Leave off cream cheese frosting and instead sprinkle tops with cinnamon and coarse sugar.

To make gluten free: Try using chickpea flour or an all purpose gluten free flour. I have not tried this option, but am quite certain it would work.

Important notes about nutrition: The nutrition information provided includes everything except raisins and shredded coconut. If you add both, your muffins will be around 200 calories of good nutrition.

Servings: 12 muffins
Serving size: 1 muffin (with glaze but without mix-ins)
Calories: 180kcal
Fat: 3.9g
Saturated fat: 1.6g
Carbohydrates: 34.4g
Fiber: 2.5g
Sugar: 22g
Protein: 2.8g


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Healthy carrot cake muffins

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