Carrot Cake Protein Muffins

12 muffins
35 min

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These Carrot Cake Protein Muffins are tender, subtly sweet, and packed with protein. Made from protein pancake mix, the muffins are perfect for breakfast!

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While muffins are delicious, most pack on the calories with little nutritional value. These carrot cake protein muffins vary away from that characteristic, as they are made with protein pancake mix. And hey, there are vegetables (carrots) in the muffins too!

What makes these protein muffins?

Firstly, these carrot cake protein muffins are made using a protein pancake mix. Typically protein pancake mixes are made from whole wheat, almond, or oat flour. And they will have the addition of a protein blend which could include protein isolates, whey protein, or another form of protein powder.

Additionally, the muffins contain eggs, Greek Yogurt, and nuts. All of which contain high amounts of protein.

Ingredients & Substitutions

  • Instead of flour, this recipe uses protein pancake mix. Feel free to use your favorite brand. My go-to is always Kodiak Cakes.
  • The carrots need to be grated, by hand with a box grater, or in a food processor. Keep in mind when using a food processor, that you will need to keep a close eye on the carrots to avoid turning them into mush. While I used regular carrots, baby carrots work well too. *Do not use pre-shredded store-bought carrots here, they do not have the same moisture level as freshly grated.
  • This recipe calls for avocado oil as the fat, but liquid coconut oil would be great here as well.
  • Nuts are ultimately optional, the recipe calls for pecans, but they do add a lovely crunch. Another great addition to these muffins would be raisins or dried cranberries.
  • The cream cheese icing is a lovely combination of cream cheese, unsalted butter, confectioners' sugar, and vanilla extract. There is just enough icing on each muffin for the perfect level of sweetness.


  1. Combine the dry ingredients.
  2. Add the wet ingredients into the dry ingredients and mix until everything is just combined. (Do not over-mix.)
  3. Fold in the carrots and nuts.
  4. Bake for 20 minutes and cool. *Do not leave the muffins in the tin to cool completely. After removing the muffins from the oven, cool them in the tin for about 10 minutes before transferring the muffins to a cooling rack.
  5. Make the cream cheese icing and frost the completely cooled carrot cake muffins.
  6. Store muffins in an airtight container in the refrigerator for up to 5 days.

Frequently Asked Questions

What happens if the muffin batter is over-mixed? When muffin batter is mixed too much, it crushes the air bubbles and ruins the integrity of the fluffy texture. As a general rule of thumb, mix the dry and wet ingredients just until the dry ingredients are no longer visible.

Why are the carrots folded in? In order to incorporate the heavy carrots into the batter without deflating the air, they are folded in at the end of the mixing process.

Can carrot cake muffins be frozen? Yes, you can freeze these muffins. The best practice is to freeze the muffins prior to icing them, as the icing can lose its shape after thawing. Place the unfrosted muffins in an airtight container or freezer-safe zip-top bag. Freeze for up to 3 months.

Do these carrot cake muffins need to be refrigerated? Yes, because of the cream cheese icing the muffins do need to be refrigerated. Store the muffins in the refrigerator in an airtight container for up to 5 days.

Do these muffins taste like carrot cake? These protein muffins have all the goodness of carrot cake but in a muffin form.

These carrot cake protein muffins are subtly sweet and oh so yummy. They are perfect for breakfast or as a healthy dessert. And, these muffins are a great match for a cup of coffee.

DID YOU MAKE THIS RECIPE? Please leave a star rating and review on my website!

Carrot Cake Protein Muffins
Recipe details
  • 12  muffins
  • Prep time: 15 Minutes Cook time: 20 Minutes Total time: 35 min
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  • 2 cups protein pancake mix I used Kodiak Cakes.
  • 1/2 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 teaspoon ground cinnamon
  • 3/4 cup light brown sugar packed
  • 2 large eggs room temperature and beaten
  • 1/2 cup avocado oil or liquid coconut oil
  • 1/3 cup plain Greek yogurt
  • 1 teaspoon pure vanilla extract
  • 1 1/2 cups grated carrots
  • 1/2 cup chopped pecans or chopped walnuts
Cream Cheese Icing
  • 2 oz cream cheese softened
  • 2 oz unsalted butter softened
  • 1/2 teaspoon pure vanilla extract
  • 1/2 cup confectioners' sugar (powdered sugar), sifted
  • 2 tablespoon milk or half and half
For the Muffins
Preheat the oven to 350° F and grease a 12 cup muffin tin, or line with paper liners.
In a large mixing bowl, combine the pancake mix, baking soda, baking powder, cinnamon, salt, and brown sugar, stir to combine.
Add the beaten eggs, avocado oil, Greek yogurt, and vanilla extract. Mix until everything is just incorporated, do not over-mix. Fold in the carrots and pecans.
Fill each cup of the prepared muffin tin ¾ of the way full. Bake for about 20 minutes, or until a toothpick inserted into the center comes out clean. Allow the muffins to cool for about 10 minutes before transferring them to a rack to cool completely.
For the Cream Cheese Icing
In the bowl of a standing mixer, or a large bowl with a hand mixer, beat together the cream cheese and butter until light and fluffy. Add the vanilla extract and confectioners' sugar, beat until smooth. Beat in the milk or half and half, mixing until completely incorporated.
Evenly distribute the icing onto each muffin and carefully spread the icing with a spatula until the top surface is covered.
Store muffins in the refrigerator in an airtight container for up to 5 days.
Katelyn | Sugary Logic
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  • Robyn Robyn on Oct 10, 2021

    Do you have a gluten free recipe pls

  • Sharon V Sharon V on Nov 17, 2021

    Can this be made keto friendly?

    • Katelyn | Sugary Logic Katelyn | Sugary Logic on Nov 23, 2021

      Hi, Sharon! I apologize for the delayed response; I was unwell last week.

      You can certainly use a keto pancake mix, and either monk fruit sweetener or stevia in place of the sugar. It is important to note that carrots are naturally high in carbohydrates compared to other vegetables.