Healthy protein carrot cake muffins are the perfect protein muffin for spring! Made with fresh carrots, warm spices, and pecan coconut topping, this carrot cake muffin is moist, fluffy, and delicious. Make them ahead for a healthy breakfast or easy snack.

Want this recipe sent to you?
Jump to:
Why You Should Make These Muffins
- Great for meal prep: Store well both at room temperature and in the freezer.
- High-protein and less sugar: Each protein carrot cake muffin has 14 grams of protein per muffin. Only 6.7 grams of sugar per muffin.
- Delicious breakfast or snack: A yummy and healthy breakfast, or snack that tastes like carrot cake, but with added protein and wholesome ingredients.
- Great for spring holidays and parties: Easy to bake for spring holidays like Easter brunch or Mother's Day.
Ingredients
Here are the ingredients you need to make this recipe. Reference the recipe card at the bottom for exact measurements and the notes below for substitution ideas.

- Protein pancake mix: Protein pancake mix like Kodiak Cakes makes great muffins. That is what I use in my Kodiak Cakes blueberry muffins, protein waffles, and my microwave pancake. I even use it in my air fryer crispy chicken!
- Protein powder: I recommend Orgain Plant-based vanilla protein powder.
- Pecans: Chopped pecans add a delicious crunch topping. Walnuts also work.
- Shredded coconut: I love adding a bit of shredded coconut to the top of the muffins. You can omit it if you don't care for coconut.
- Eggs: Eggs provide moisture, protein, and structure to these muffins.
- Crushed pineapple: Crushed pineapple is a standard in carrot cake and adds a delicious flavor and sweetness.
- Shredded carrots: Shred the carrots on the small grate side for better texture. If using pre-shredded carrots, pulse them in a food processor prior to adding to the batter.
- Coconut oil: Refined coconut oil removes the strong coconut taste. You can also use butter if needed.
- Maple syrup: Maple syrup naturally sweetens these protein carrot cake muffins. You can also use honey or brown sugar if you prefer.
- Almond milk: Almond milk helps to bring the muffin batter together and provides moist texture.
- Cinnamon: Cinnamon adds warm spice.
- Vanilla extract: Vanilla extract gives baked goods a delicious, warm flavor.
See recipe card for quantities.
How to Make Carrot Cake Protein Muffins
Below are step-by-step instructions for how to cook this recipe with the best results. The recipe card at the bottom shows the exact cooking time and temperatures.

Step 1: Dry Ingredients
Preheat the oven to 425°F. In a large bowl, combine the dry ingredients with a whisk.

Step 2: Whisk Eggs
Whisk one large egg in a separate medium bowl.

Step 3: Add Remaining Wet Ingredients
Add the remaining wet ingredients to the bowl. Fold in the carrots.

Step 4: Wet Into Dry
Gently stir the wet ingredients into the dry ingredients until just mixed. Add additional almond milk (1 teaspoon at a time) if needed.

Step 5: Ready to Bake
Evenly scoop 10 muffins into a muffin tin lined with muffin liners. Top each muffin with chopped pecans and coconut shreds.
Bake at 425°F for 5 minutes and at 350°F for 15 minutes. Cool muffins on a wire rack.
Hint: Use a large muffin scoop to make bakery-style muffins!
Substitutions
- Gluten-free - use gluten-free dry ingredients or substitute protein pancake mix for gluten-free oat flour.
- Dairy-free - use oat flour in place of protein pancake mix (most are made with whey protein).
- Egg-free - Substitute the egg with ¼ cup applesauce.
Variations
- Cream cheese frosting - Skip the nut topping and instead top the a combination of 4 oz. softened cream cheese, 1-2 tablespoons of milk, and 2 tablespoon of powdered sugar. That's what I top my Gingerbread loaf and Pumpkin Cake with!
- Raisins - Raisins add additional natural sweetness. Stir in ½ cup of raisins into the muffin batter.
- Orange - add 1 tablespoon of orange zest to the muffin batter.
See this carrot cake loaf or this carrot cake baked oats recipe on my website for a similar recipe!
Equipment
To make these protein carrot cake muffins, you'll need a muffin tin, muffin liners, and a large cookie or muffin scoop.
Storage
Store cooled protein muffins in an airtight container at room temperature for 3-4 days.
Freeze cooled muffins in a freezer-safe container for up to 3 months.
Top Tip
Finely grate the carrots for the best texture and moisture!
Recipe FAQs
I usually add blended cottage cheese or Greek yogurt to muffins to add protein. You may need to add more protein pancake mix if adding additional liquid.
No. The protein powder mixes well with the dry ingredients. I cannot taste anything other than carrot cake muffins!
Yes, however, it will impact the amount of protein. You can omit protein powder and adjust the almond milk as needed.

More Healthy Protein Muffins to Bake!
Looking for other protein muffin recipes? Try these:
If you've made this recipe, would you please leave a star rating and comment below on the recipe card? If you want more simple + delicious eats, please subscribe to my newsletter and follow along on Facebook, Pinterest, and Instagram for the latest updates.
Healthy Protein Carrot Cake Muffins
Equipment
Ingredients
- 2 cups Kodiak Cakes Flapjack Mix
- 4 scoops Orgain vanilla protein powder
- 1 teaspoon cinnamon
- 1.5 cups almond milk
- ¼ cup maple syrup more for sweeter muffins
- ¼ cup refined coconut oil melted
- 1 teaspoon vanilla extract
- 1 large egg
- ½ cup shredded carrots
- 2 tablespoon chopped pecans
- 2 tbsp shredded coconut
Instructions
- Preheat the oven to 425°F. Prepare a muffin tin with muffin liners and spray them with coconut oil spray.
- Combine the dry ingredients in a large bowl.2 cups Kodiak Cakes Flapjack Mix, 4 scoops Orgain vanilla protein powder, 1 teaspoon cinnamon
- In a separate medium bowl, add the egg and beat it with a whisk. Stir in the other liquid ingredients until well mixed.1.5 cups almond milk, ¼ cup maple syrup, ¼ cup refined coconut oil, 1 large egg, 1 teaspoon vanilla extract
- Stir in the carrots.½ cup shredded carrots
- Use a large cookie scoop to scoop out approximately 10 large muffins into a prepared muffin tin. Top each muffin with a sprinkle of pecans and coconut.2 tablespoon chopped pecans, 2 tablespoon shredded coconut
- Bake the muffins for 5 minutes. Lower the oven temperature to 350°F and bake for an additional 15 minutes or until a toothpick inserted into the center of a muffin comes out clean.











Leave a Reply