Healthy Carrot Cake Muffins

Healthy Carrot Cake Muffins

Healthy & Easy Carrot Cake Muffins Recipe

Looking for a protein muffins recipe that actually tastes good? This Healthy Carrot Cake Muffins recipe is amazing! Made with no refined sugar or grain, these delicious protein muffins will help you start the day off right!

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Healthy carrot cake muffins with cream cheese frosting and walnuts.

How to Make Healthy Carrot Cake Muffins

If you loved my Blueberry protein muffins, then you’ll adore this scrumptious Carrot Cake Muffin recipe. With the same flavor as the classic carrot cake, these muffins include shredded carrots, walnuts and cinnamon, but without the refined sugar and flour or oil.

I’ve amped up the protein in these healthy carrot cake muffins by including eggs, Greek yogurt and collagen protein. I also substitute oat flour for the traditional bleached all-purpose flour to provide additional protein and fiber.


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Ingredients for healthy carrot cake muffins recipe

What do I need to make healthy carrot cake muffins?

Here’s a list of the ingredients you’ll need to make this carrot cake muffin recipe:

  • Oat flour (you can make this by simply blending or processing old fashioned oats.)
  • Unflavored collagen protein
  • Granular sweetener – I like Lakanto Monk Fruit Sweetener
  • Baking Powder
  • Cinnamon
  • Nutmeg
  • Milk (feel free to use dairy or plant-based milk)
  • Plain Greek yogurt
  • Eggs
  • Vanilla extract
  • Shredded carrots
  • Chopped walnuts

Oat flour to make healthy pumpkin pancakes.

How do you make oat flour?

There is no need to buy oat flour. You can make oat flour in your blender or food processor. Simply add old fashioned (not instant) oats, and blend or process until flour form. 

I have a Blendtec Designer Series Blender. It takes approximately 30-45 seconds to achieve flour consistency. You can get a 20% discount off this Blendtec blender by entering the discount code DELIGHTFULEMADE at check out.

Wet, dry ingredients and batter for healthy carrot cake muffins recipe.

Mix the wet and dry ingredients to create the muffin batter

In separate bowls, mix the wet and dry ingredients. Gradually add the dry ingredients to the wet. Once your batter is mixed, fold in the shredded carrots and walnuts.

What can I add to the carrot cake muffins to make them sweeter?

A couple of great options to add sweetness to this protein muffin recipe is raisins (red or golden) and/or crushed pineapple. Some people also like shredded coconut in their carrot cake. To keep this recipe healthy, make sure you’re choosing ingredients that are not adding extra refined (added) sugar. Check your labels.


Muffin batter in pan for healthy carrot cake muffins recipe

Baking these Healthy Carrot Cake Muffins

Once your batter is mixed, it is ready to go into a muffin tin. I like these silicone baking cups. They fit right into a traditional muffin/cupcake pan, and you don’t need to use any non-stick spray to your recipe. Those baking sprays are often made with unhealthy, toxic oils.

Fill the baking cups with batter and bake at 350 degrees. It’s okay to fill the cups nearly full with the batter. The muffin batter is very thick. They will rise slightly but will not over-run the cups.

Baked carrot cake muffins recipe in muffin tin.

What can I top carrot cake muffins with?

I tried a couple of different toppings for these healthy carrot cake muffins:

  • Chopped walnuts: not only do the walnuts add a great crunch to the muffins, they are a traditional ingredient in carrot cake. The flavors pair well!
  • Cinnamon Cream Cheese Frosting: to ensure that I keep these muffins healthy, I mixed together the following:
  • Unsweetened flake coconut – toasted adds some nice color!

(For the exact ingredient amounts, be sure to reference the recipe below.)

The cream cheese topping was fantastic, and not overly sweet. It was very similar to a flavored cinnamon walnut cream cheese that you would add to a bagel. It was a fantastic way to enjoy this protein muffin!

Healthy carrot cake muffins topped with cream cheese frosting and walnuts.

If you loved this delicious Protein Muffins recipe, check out some of my other similar recipes:

Blueberry Protein Muffins

Healthy Apple Muffins

Healthy Blueberry Pancakes – also made with Oat Flour!

Pumpkin Chocolate Chip Protein Muffins

Blueberry Overnight Oats

Pumpkin Spice Protein Shake

Easy Mocha Protein Shake at Real Housemoms


Here’s the recipe for these delicious Healthy Carrot Cake Muffins:

Serves 12 muffins

Healthy Carrot Cake Muffins

Looking for a protein muffins recipe that actually tastes good? This Healthy Carrot Cake Muffins recipe is amazing! Made with no refined sugar or grain, these delicious protein muffins will help you start the day off right!

15 minPrep Time

30 minCook Time

45 minTotal Time

Save RecipeSave Recipe


  • 2 c. oat flour
  • 1/3 c. unflavored collagen protein
  • 1/4 c. granular monk fruit sweetener, like Lakanto
  • 1 1/2 tsp. cinnamon
  • 1 tsp. baking powder
  • 1/2 tsp. nutmeg
  • 1/4 tsp. salt
  • 1 c. milk (dairy or plant-based)
  • 3/4 c. plain Greek yogurt (like Fage 5%)
  • 2 eggs
  • 1 tsp. vanilla extract
  • 1 c. shredded carrots
  • 1/2 c. chopped walnuts, plus more for optional muffin topping
  • Cream Cheese Topping:
  • 8 oz. (1 pkg.) cream cheese, room temperature
  • 2 Tbsp. monk fruit granular sweetener
  • 1 tsp. cinnamon
  • 1 tsp. vanilla extract


  1. Preheat oven to 350 degrees. Fit a muffin tin with non-stick silicone baking cups or spray with a non-stick coconut oil spray. Set prepared pan aside.
  2. In a smaller mixing bowl, combine the dry ingredients: oat flour, collagen protein, sweetener, baking powder, cinnamon, nutmeg and salt. Whisk together to combine.
  3. In a second larger bowl, combine the wet ingredients: Milk, Greek yogurt, eggs and vanilla extract. Whisk together to combine. Gradually add the dry ingredients to the wet ingredients and stir together until well incorporated. Batter will be slightly thick. Fold in the shredded carrots and chopped walnuts.
  4. Spoon the batter into the prepared pan, filling each cup to nearly full. The muffins will rise while baking, but will not spill over the cups. Optional: top each muffin with additional chopped walnuts.
  5. Bake at 350 degrees for 28-30 minutes. Muffins will be golden brown. Remove from oven and let cool for 10 minutes before removing from pan.
  6. Optional Cream Cheese Topping: While the muffins cool, mix together the room temperature cream cheese, cinnamon, granular sweetener, and vanilla. Mix until well combined and smooth - there should be no lumps. Spread on top of the cooled muffins. Add additional chopped walnuts or flake coconut, if desired.


Serving size: 1 muffin

Optional add ins: 1/2 c. red or golden raisins, 1/2 c. unsweetened flake coconut

Freezing directions: To freeze place muffins in airtight container, or wrap individually and freeze. Defrost at room temperature overnight, or on defrost setting in microwave. If freezing muffins, wait to top with cream cheese topping until just before serving.


soy free
seafood free
sesame free
mustard free


Healthy carrot cake muffins recipe topped with cream cheese frosting.

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