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healthy carrot cake muffins

Healthy Carrot Cake Muffins

These Healthy Carrot Cake Muffins are glorious! They are wholesome and delicious, making this healthy muffin recipe one of my favorites! 
5 from 1 vote
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Course: Breakfast
Cuisine: American
Keyword: carrot cake muffins, carrot muffins, healthy carrot cake muffins
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes
Servings: 12
Calories: 213kcal


  • 1 cup white whole-wheat flour
  • ½ cup oat flour
  • 1 teaspoon baking powder
  • 1 teaspoon cinnamon
  • ½ teaspoon salt
  • 2 large eggs
  • 3/4 cup coconut palm sugar
  • 1 cup crushed pineapple drained
  • 1 teaspoon pure vanilla extract
  • ¼ cup melted coconut oil
  • 3/4 cup almond milk any non-dairy or dairy milk can be substituted.
  • 1 cup grated carrots
  • 1/2 cup chopped pecans
  • ½ cup unsweetened shredded coconut plus 2 tablespoons


  • Preheat oven to 350 degrees
  • In a large mixing bowl combine flours, baking powder, cinnamon, and salt. Set aside.
  • In another large mixing bowl whisk together eggs and coconut palm sugar until smooth and blended.
  • Then whisk in the crushed pineapple and vanilla extract.
  • Slowly whisk in the melted coconut oil and milk.
  • Make a well in the center of the flour mixture and pour in the wet ingredients. Slowly stir gently by hand until all the ingredients are blended and the flour mixture is moist. Please note at this time the batter will be very wet.
  • Slowly fold in the carrots, coconut, and nuts. The batter at this time will be a little thicker and resemble more of a muffin batter.
  • Spray a 12-cup muffin pan with cooking spray. Divide the batter among the muffin cups. I used a cookie scoop and filled each muffin cup with two scoops. This worked out quite well and made the muffins very even. Divide the 2 tablespoons of coconut evenly over the 12 muffins.
  • Bake the muffins for 20 -25 minutes or until a toothpick comes out clean after being inserted. Let the muffins sit in the pan for about 5 minutes and then take out of the pan and place them on a wire rack to finish cooling.


Cooking notes

To melt the coconut oil, place the desired amount into a glass measuring cup and microwave until melted. If you end up with too much coconut oil, pour the extra back into the coconut oil jar.

How to Store, Reheat, and Freeze

Muffins are a meal prep superstar! I think most muffin recipes, especially this healthy carrot cake muffin recipe, get better the next day or after it’s frozen. Yup! The flavors get a chance to marry together and are more delicious than the day you made them.
The most important thing is to let the muffins cool completely before storing or freezing them. Doing it this way prevents the muffins from getting soggy or ice crystals forming when freezing.
Then store muffins at room temperature in a plastic or glass container. Put a paper towel underneath the muffins to absorb any excess moisture. Muffins will keep up to 4 days this way. If you want muffins to last longer, then freeze them.
To freeze muffins, place them together into a freezer bag and lay flat in the freezer. This will keep the muffins from sticking together. After the muffins are frozen, place the bag wherever you want in the freezer.
You can also wrap the muffin individually in plastic wrap before adding it to a freezer bag. If you plan to take the muffins on the go for lunch or snacks, having them wrapped will be helpful. 
I recommend letting them thaw on the counter; this takes about 20 minutes. You can also reheat the muffins in the microwave. Heat in 10-second increments until the muffin thaws.


Serving: 1muffin | Calories: 213kcal | Carbohydrates: 29g | Protein: 3g | Fat: 9g | Saturated Fat: 5g | Fiber: 3g | Sugar: 17g