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    Home » Recipes » Cakes and Cupcakes

    The Best Protein Cupcakes (Healthy)

    Published: Aug 24, 2022 · Modified: Jan 21, 2025 by Crystal Yentzen · This post may contain affiliate links · 16 Comments

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    Healthy Protein Cupcakes

    Pump up your protein with these healthy protein cupcakes! Vanilla flavored cupcakes with a protein cream cheese frosting made with wholesome ingredients. Plus, they're super easy to make!

    a healthy protein cupcake with cream cheese frosting and sprinkles

    I am happy to share that I partnered with Naked Nutrition to bring you these delicious protein-filled cupcakes! Their Grass-Fed Whey Protein Powder bakes up perfectly in this recipe and is an excellent addition to every baker's kitchen. Bring on the healthy desserts!!

    I love creating healthy dessert recipes with all the flavor and texture we expect from the classic version. You know, the kind of dessert where you ask yourself, "Is this really healthy?"

    Don't get me wrong; these cupcakes don't taste like traditional buttercream cupcakes. But the texture and flavor are very similar.

    You may have difficulty believing they're made with ground oats and whey protein powder. Now let's talk about the health benefits.

    Jump to:
    • Are these cupcakes healthy?
    • Ingredients
    • Instructions
    • Recipe FAQs
    • Want more protein dessert recipes?
    • 📖 Recipe
    • 💬 Comments

    Are these cupcakes healthy?

    The answer: Yes! Here are five reasons why:

    1. We replace the butter in traditional cupcakes with olive oil. Olive oil is an excellent source of antioxidants and healthy fats. I bake with it all the time, and no one ever suspects.
    2. They are refined sugar-free. I use Sweetleaf Stevia Drops and maple syrup to sweeten the cupcakes. Stevia is a natural sugar substitute with zero calories. Maple syrup and stevia give the perfect amount of sweetness without a ton of sugar.
    3. No flour! We use oat flour instead, which is just old-fashioned ground oats. Oats are whole grain and full of fiber and nutrients our bodies need.
    4. Each cupcake has 9 grams of protein! Protein is essential for building and maintaining lean muscle mass, and if you can get it in a cupcake- why not?
    5. Did I mention that Naked Whey Protein Powder is sourced from grass-fed cows? This is so important because not only is it better for the animals and environment, but it's also healthier for us. If you're interested, here is more about the health benefits of grass-fed whey.

    a protein cupcake with a bite taken out of it

    Ingredients

    All of the recipe ingredients are easy to find. Here's what you'll need:

    For the cupcakes:

    ingredients to make protein cupcakes
    • Oat Flour–  Oat flour is sold in stores, but it's also super easy to make at home. Simply blend old-fashioned oats in a high-speed blender until the oats become a fine powder (about 30 seconds to a minute). Store your oat flour in an air-tight container for up to three months. 
    • Whey Protein Powder- I recommend Naked Whey from Naked Nutrition. They source from small dairy farms where the cows are grass-fed and raised without growth hormones. Plus, their whey protein powder is free of any additives. I love to bake with it and add it to smoothies.
    • Cornstarch- A small amount of cornstarch helps to thicken and bind the cupcakes.
    • Baking Powder- You'll need baking powder to help the cupcakes rise. Be sure to use fresh baking powder that's not expired. Not sure? To test your baking powder, mix a small amount with a few tablespoons of hot water. If it fizzes, it's still good.
    • Salt- Any fine grain salt will do.
    • Maple Syrup and Stevia- I use Sweetleaf Stevia Drops and maple syrup to sweeten the cupcakes. Stevia is a natural sugar substitute with zero calories. There are many different brands on the market, so feel free to use whichever you prefer. Just read the label and add the equivalent of ½ cup of sugar. If you choose to omit the stevia, you will need to add ½ cup of any granulated sweetener. I do not recommend adding more maple syrup because it will mess up the wet-to-dry ratio. 
    • Egg- You'll need one large egg, and I always recommend buying pasture-raised eggs. They are the healthiest and kinder to the animals.
    • Olive Oil- As I said, I use olive oil for its health benefits, but feel free to use canola or vegetable oil if that's what you have.
    • Milk- Regular dairy or plant-based milk (like almond milk) will work just fine.
    • Vanilla Extract- Pure vanilla extract is best, but imitation works too.

    For the frosting

    Ingredients to make protein frosting
    • Cream Cheese- I use the reduced fat (Neufchatel) cream cheese. Of course, you can go with full-fat if you prefer.
    • Greek Yogurt- Get a thick brand such as Fage or Chobani, and be sure that it's unsweetened.
    • Maple Syrup and Stevia- Like the cupcakes, I use Sweetleaf Stevia Drops and maple syrup to sweeten the frosting. I think combining the two lends the best flavor, as stevia alone can be a bit bitter. If you choose to omit the stevia for the frosting, add ¼ cup of any powered sweetener such as regular confectioner's sugar. 
    • Whey Protein Powder- I use the same Naked Whey Protein Powder for the frosting and cupcakes.
    • Vanilla Extract- Pure vanilla extract is best, but imitation works too.
    • Salt- Don't forget a pinch of salt.

    Instructions

    Prepare the Cupcakes

    • In a large bowl, sift or whisk together the oat flour, whey protein powder, cornstarch, baking powder, and salt. I recommend sifting for the best texture. Set aside.
    • In a medium-sized bowl, whisk together the maple syrup, egg, olive oil, milk, vanilla extract, and stevia.
    • Pour the wet mixture into the dry mixture and mix until everything is just incorporated. Allow the batter to rest for 5 minutes.
    • Stir the batter once more, and divide it between the lined muffin cups. Bake for 11-13 minutes. Mine were perfect at 12 minutes. Allow the cupcakes to cool for 5 minutes in the muffin tin before transferring them to a wire rack to cool completely.

    cupcakes cooling on a wire rack

    Prepare the frosting:

    • In a large bowl, using a handheld or stand mixer fitted with a paddle or whisk attachment, beat the cream cheese and Greek yogurt on medium until smooth and creamy. Be sure to stop and scrape down the sides and bottom of the bowl as necessary.
    • Add the maple syrup, protein powder, stevia, vanilla extract, and salt. Beat on low for 30 seconds and then on high for 2 minutes or until light and fluffy. Cover and refrigerate for at least an hour.
    • Frost your cupcakes as desired. This is a loose frosting, so if you want to pipe it on, I recommend using a large round tip. I use the Wilton 1A Round Decorating Tip.

    a close-up shot of a vanilla protein cupcake with frosting and sprinkles

    Recipe FAQs

    Can I use a different protein powder?

    I tested this recipe using Naked Whey Protein Powder from Naked Nutrition, which is free from added sweeteners. If you use a sweetened whey protein powder, you may want to reduce the amount of stevia in the recipe.

    What type of muffin tin is best to use?

    Aluminum muffin pans work best for baking cupcakes. Aluminum heats up quickly and evenly, ensuring that your cupcakes come out perfectly every time. It's also durable and resistant to warping. I love mine!

    Can I make the cupcakes ahead of time?

    Yes, you can make the cupcakes and frosting one day ahead of time. Store the cupcakes covered at room temperature and the frosting covered in the refrigerator.

    Want more protein dessert recipes?

    Check these out:

    Double Chocolate Protein Mug Cake (made with oats)

    Healthy Protein Brownies

    Peanut Butter Protein Cookies

    Silken Tofu Pudding (Easy)

    Banana Protein Cookies

    Chocolate Banana Protein Muffins

    Please let me know how you like the protein cupcakes in the comments. Your feedback means a lot to me, and your star ratings encourage other readers to try this recipe.

    Enjoy!

    Crystal

    📖 Recipe

    Healthy Protein Cupcake
    Print Recipe
    4.66 from 40 votes

    The Best Protein Cupcakes (Healthy)

    Pump up your protein with these healthy protein cupcakes! Vanilla flavored cupcakes with a protein cream cheese frosting made with wholesome ingredients. Plus, they're super easy to make!
    Prep Time20 minutes mins
    Cook Time15 minutes mins
    chill frosting1 hour hr
    Total Time1 hour hr 35 minutes mins
    Course: Dessert
    Cuisine: American
    Keyword: high protein, Oat flour
    Servings: 12
    Calories: 205kcal
    Author: Crystal Yentzen

    Ingredients

    Protein Cupcakes

    • 1 cup oat flour*
    • ½ cup whey protein powder* from Naked Nutrition, see notes
    • 3 tablespoons cornstarch
    • 2 and ¼ teaspoon baking powder
    • ½ teaspoon salt
    • ½ cup maple syrup
    • 1 egg
    • 4 and ½ tablespoons olive oil
    • ⅓ cup milk of choice
    • 1 tablespoon vanilla extract
    • 1 teaspoon stevia* or sweetener of choice, see notes

    Protein Frosting

    • 8 oz light cream cheese
    • ¾ cup Greek Yogurt plain and unsweetened
    • ¼ cup maple syrup
    • 2 scoops (6 and ½ tablespoons) whey protein powder from Naked Nutrition, see notes
    • 1 teaspoon vanilla extract
    • ⅛ teaspoon salt
    • ¼ teaspoon stevia* or to taste, see notes

    Instructions

    Prepare Cupcakes

    • Preheat the oven to 350°F (177°C). Line a 12-cup muffin pan with cupcake liners and spray them lightly with non-stick spray.
    • In a large bowl, sift or whisk together the oat flour, whey protein powder, cornstarch, baking powder, and salt. I recommend sifting for the best texture. Set aside.
    • In a medium-sized bowl, whisk together the maple syrup, egg, olive oil, milk, vanilla extract, and stevia.
    • Pour the wet mixture into the dry mixture and mix until everything is just incorporated. Allow the batter to rest for 5 minutes.
    • Lightly stir the batter once more, and divide it between the lined muffin cups. Bake for 11-13 minutes. Mine were perfect at 12 minutes. Allow the cupcakes to cool for 5 minutes in the muffin tin before transferring them to a wire rack to cool completely.

    Prepare Frosting

    • In a large bowl, using a handheld or stand mixer fitted with a paddle or whisk attachment, beat the cream cheese and Greek yogurt on medium until smooth and creamy. Be sure to stop and scrape down the sides and bottom of the bowl as necessary.
    • Add the maple syrup, protein powder, stevia, vanilla extract, and salt. Beat on low for 30 seconds and then on high for 2 minutes or until light and fluffy. Cover and refrigerate for at least an hour.
    • Frost your cupcakes as desired. This is a loose frosting, so if you want to pipe it on, I recommend using a large round tip. I use the Wilton 1A Round Decorating Tip.
    • Enjoy!

    Notes

    1. Oat Flour–  Oat flour is sold in stores, but it’s also super easy to make at home. Simply blend old-fashioned oats in a high-speed blender until the oats become a fine powder (about 30 seconds to a minute). Store your oat flour in an air-tight container for up to three months. 
    2. Whey Protein Powder- I use Naked Whey Grass-Fed Protein Powder from Naked Nutrition for this recipe, which is free from additives and sweeteners. If you use a sweetened whey protein powder, you may want to reduce the amount of stevia in the cupcakes. 
    3. Stevia for Cupcakes- I use Sweetleaf Stevia Drops and maple syrup to sweeten the cupcakes.  Stevia is a natural sugar substitute with zero calories. There are many different brands on the market, so feel free to use whichever you prefer. Just read the label and add the equivalent of ½ cup of sugar. If you choose to omit the stevia, you will need to add ½ cup of any granulated sweetener. I do not recommend adding more maple syrup because it will mess up the wet-to-dry ratio. 
    4. Stevia for Frosting-  Like the cupcakes, I use Sweetleaf stevia drops and maple syrup to sweeten the frosting. Combining the two lends the best flavor, as stevia alone can be a bit bitter. If you choose to omit the stevia for the frosting, add ¼ cup of any powered sweetener such as regular confectioner's sugar or powdered monk fruit.
    5. Store your prepared cupcakes at room temperature for one day or in the refrigerator for up to 4 days.

    Nutrition

    Calories: 205kcal | Carbohydrates: 25g | Protein: 5g | Fat: 10g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 5g | Trans Fat: 0.003g | Cholesterol: 24mg | Sodium: 213mg | Potassium: 230mg | Fiber: 1g | Sugar: 14g | Vitamin A: 125IU | Calcium: 112mg | Iron: 1mg

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    Reader Interactions

    Comments

    1. Gina Abernathy says

      August 24, 2022 at 9:44 pm

      5 stars
      These will be so pretty for a birthday party this weekend.

      Reply
    2. Andrea White says

      August 24, 2022 at 11:32 pm

      5 stars
      love that these cupcakes are protein-packed! so good!

      Reply
    3. Sarah says

      August 25, 2022 at 8:35 am

      5 stars
      How cute are these?? Such fun colors, you'd never know they were healthy! That means I can eat two right? 🙂

      Reply
      • Crystal Yentzen says

        August 25, 2022 at 11:53 am

        Haha! Yes, go right ahead!

        Reply
    4. Katie says

      September 18, 2022 at 1:21 pm

      5 stars
      These protein cupcakes are so delicious oh my goodness1 The perfect healthy treat!

      Reply
      • Crystal Yentzen says

        September 18, 2022 at 1:58 pm

        I'm so glad you like them!

        Reply
    5. Jess says

      September 19, 2022 at 1:33 am

      5 stars
      These are so perfect and delish

      Reply
    6. Nancy says

      September 19, 2022 at 5:04 pm

      5 stars
      Wow awesome these cupcakes has extra protein to make it less unhealthy

      Reply
    7. Susan says

      December 27, 2022 at 12:42 am

      Oven temp ?

      Reply
      • Crystal Yentzen says

        December 27, 2022 at 1:20 am

        The oven should be heated to 350°F. I've added that to the instructions. Thanks so much!

        Reply
    8. Kasi says

      April 14, 2023 at 4:54 pm

      can you substitute almond flour for the oat flour?

      Reply
      • Crystal Yentzen says

        April 15, 2023 at 2:21 pm

        Almond flour will give the cupcakes a different consistency because it has a higher fat content than oat flour. They probably wouldn't rise as well. I hope that helps!

        Reply
    9. Atisha Reliford says

      June 29, 2024 at 6:09 pm

      5 stars
      A must try!

      Reply
      • Crystal Yentzen says

        July 02, 2024 at 4:14 pm

        I'm so happy you like the cupcakes!

        Reply
    10. Carolyn Mraz says

      May 11, 2025 at 12:37 am

      Can you use a plant based protein powder instead of whey?

      Reply
      • Crystal Yentzen says

        May 14, 2025 at 8:09 pm

        Plant-based protein powders tend to be more absorbent than whey, so if you decide to use plant-based, add a splash (like 2-3 tablespoons) of your milk of choice. Let me now how they turn out!

        Reply
    4.66 from 40 votes (33 ratings without comment)

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