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    Home » Recipes » Gluten Free Dairy Free Desserts

    Dairy-Free Protein Cupcakes (Gluten-Free)

    Modified: Jun 4, 2025 · Published: Feb 27, 2023 by Shelby Stover · This post may contain affiliate links · 42 Comments

    Jump to Recipe
    Two images of vanilla protein cupcakes with text between the top a close up of one with a bite out of it and the bottom of multiple lined up.
    Vanilla protein cupcake with dairy-free frosting and sprinkles in a blue cupcake liner with more cupcakes behind it on a cutting board.

    Enjoy what you eat guilt-free and boost your daily protein intake with these protein cupcakes! Soft, light, and full of fuel these gluten-free cupcakes are worth waiting for.

    Made with healthy pantry staples so they come together quickly, the protein cupcakes are topped with your favorite frosting and they the best way to celebrate.

    Vanilla protein cupcake with dairy-free frosting and sprinkles in a blue cupcake liner with more cupcakes behind it on a cutting board.

    Looking for a dessert to whip up in a pinch that everyone will enjoy?

    Why not make these protein cupcakes?

    These high protein cupcakes are the perfect blend of sweet indulgence and protein-packed fuel. Dress them up for whatever occasion and know you’re getting some nutrients in with your dessert.

    Hot tip: even people who are not protein-obsessed will love these cupcakes!

    As a Certified Nutrition Coach, I know that there’s a delicate balance between everyday healthy meals and dessert.

    However, I can’t deny that I love blending the two of them to enjoy the best of both worlds.

    Why You'll Love This Recipe

    Easy to make: the protein cupcakes use a lot of pantry staples you probably already have on hand so they're easy to whip up. Plus, no fancy kitchen techniques are needed here.

    Versatile: the cupcakes work just as perfectly as a Friday night treat as they do for a birthday party or other gathering.

    Allergy-friendly: great to bring to a party so that everyone feels included, the cupcakes are naturally dairy-free and gluten-free.

    High in protein: because these cupcakes use collagen powder, they come in with a whopping 17 grams of pure protein. Learn more about the benefits of a high protein diet and why you want to amp it up!

    Ingredients You’ll Need

    As a busy mom, it’s important to me to whip up recipes with ingredients I naturally have on hand. This is why, if you have a well-stocked gluten-free pantry, you’ll have everything you need to make these collagen protein cupcakes!

    And though you might expect some whole wheat pastry flour or cocoa powder, there's none of that in here!

    Gluten-free 1:1 baking flour: make sure to use baking flour and not all-purpose flour as the way the cupcakes rise will be different. I like Bob's Red Mill flours best.

    Collagen: one of the cleanest sources of protein and what gives these gluten-free cupcakes their high protein intake!

    Learn more about the benefits of a high protein diet as well as the difference between collagen vs protein powder.

    Egg: this helps bind the cupcakes so you do need it as I haven’t tried flax-egg in this recipe.

    Avocado oil: make sure to use avocado and not coconut oil so that the cupcakes have a consistent texture.

    Baking powder: this is what helps the cupcakes rise to perfection.

    Non-dairy milk: any plant-based milk will work. We use homemade hemp milk the most.

    Sugar: I opted for cane sugar for the recipe but I’m sure coconut palm sugar would work as well.

    Vanilla extract: the better quality your vanilla the more potent the flavor will be.

    Sprinkles: optional but always a hit in cupcakes. Grab naturally dyed sprinkles if that’s your thing.

    Mu;itple ingredients to make protein cupcakes in measuring cups with text labels.

    How To Make Protein Cupcakes

    1. Pre-heat the oven to 350 degrees Fahrenheit.
    2. In a large bowl, combine all the dry ingredients (except the sprinkles) and mix well.
    3. Add in the wet ingredients one by one and mix until no clumps remain.
    4. Line a muffin tray and portion out the batter.
    5. Bake for 25 minutes and let cool fully before icing.
    Steel bowl with eggs , collagen and flour in it.

    Step 1: Combine all the dry ingredients (except the sprinkles) for the protein cupcakes in a bowl before adding in the eggs.

    Step 2: Add in the remaining ingredients and mix well until no clumps remain.

    Raw protein cupcake batter being poured into a lined cupcake tin.
    Vanilla protein cupcakes with rainbow sprinkles in a muffin pan.

    Step 3: Portion the cupcake batter into a pre-lined muffin tin.

    Step 4: Bake for 25 minutes before removing them from the oven and letting them cool in the muffin tray.

    Frosting being piped onto a vanilla protein cupcake on a blue muffin liner with more cupcakes behind it.
    Vanilla protein cupcake with dairy-free frosting and sprinkles in a blue cupcake liner with more cupcakes behind it on a cutting board and sprinkles being poured on the cupcake.

    Step 5: Let the cupcakes cool completely while you whip up the frosting. Pipe it on.

    Step 6: Decorate the cupcakes with more sprinkles or any other add-ons you enjoy.

    Important Teaching Tips

    You cannot use chocolate protein powder for these protein cupcakes (or any protein powder). It will absorb too much liquid and the cupcakes will come out funky. Learn more about how collagen powder and protein powder differ.

    If you want to make protein cupcakes with protein powder, opt for these super-rich, chocolate protein cupcakes instead.

    The batter makes either 12 really small cupcakes or 11 normal-size ones.

    You can top the protein cupcakes with protein cupcakes frosting for a smooth, indulgent feel. If you want a chocolate protein frosting, just add a dash of cacao powder to the mixture.

    However, dairy-free cream cheese frosting or adding a double chocolate dairy-free frosting on top works too.

    Make sure to let them cool completely before icing them though.

    How To Store Protein Cupcakes

    If not frosted, these cupcakes can be stored at room temperature or in the fridge in an airtight container.

    Know that in the fridge they will become much more firm as gluten-free flour and collagen powder tend to harden a bit when stored.

    In the fridge they will last 5-7 days and on the counter they're good for up to 3 days.

    To enjoy them from the fridge, let them come to room temperature before eating or icing them.

    If the protein cupcakes recipe is iced, you need to store them in the fridge.

    Choosing Collagen Powder

    It’s no surprise that these protein cupcakes are made with collagen powder!

    All the protein without the bloat.

    I use collagen powder for amping up protein and boosting gut health.

    Learn about the difference between collagen and bone broth as how to increase protein intake.

    Honestly, as a busy mom collagen powder just makes it easy to eat more protein and not feel like I’m living off chicken and eggs.

    And more protein means more energy, more natural beauty, and feeling your BEST.

    Plus, in recipes like this, you can sneak protein into your kids as it’s one of the purest sources.

    I grab my collagen from Perfect Supplements because they source their collagen from pasture-raised (grass-fed) cows. So, I trust it. Grab some collagen powder and use code mamabear10 to save some money.

    The Best Product
    The CLEANEST Collagen Powder To Thrive
    The CLEANEST Collagen Powder To Thrive

    Easy to mix, this collagen powder adds a protein punch to anything you pair it with. Made from pasture-raised (grass-fed) cows there are no pesticides, hormones, or filler agents. Just put collagen protein. Use code mamabear10 to save money on your next order.

    Buy Now

    Frequently Asked Questions About Protein Cupcakes

    How do you store protein cupcakes?

    You can store these cupcakes on the counter in a sealed container for 1-3 days or in the fridge in a container for 3-5 days. They do become a bit crunchier in the fridge and are best eaten at room temperature.

    Can I freeze the cupcake batter?

    I have not tried prepping this protein cupcake batter ahead of time and freezing.

    Can I use flavored collagen powder?

    Sure! Know that whichever flavor of collagen powder you use will change the flavor of the cupcakes. And know what protein powder cannot be subbed in.

    Can I use protein powder instead of collagen powder?

    Though you may be able to use whey protein powder, vegan protein powder won't work for these protein cupcakes as it absorbs too much liquid.

    Are these protein cupcakes healthy?

    Though they do contain sugar, these protein cupcakes are a healthy dessert alternative. Not only are they dairy-free and gluten-free but the 17 grams of protein in them helps counter the sugar rush and keep you full longer than traditional desserts will.

    Vanilla protein cupcake with frosting and sprinkles on a blue cupcake liner with more cupcakes behind it.

    Other Protein Desserts You’ll love

    • Cinnamon sugar protein donuts
    • Collagen donuts
    • Flourless protein brownies
    • Chocolate glazed protein donuts
    • Gluten-free chocolate protein donuts
    • Cookies and cream protein shake
    • Chocolate fudge protein balls
    • High protein cookies
    • High protein pancakes
    • Chocolate protein fluff
    • High protein snack recipes
    • Gluten-free dairy-free desserts
    Vanilla protein cupcake with dairy-free frosting and sprinkles in a blue cupcake liner with more cupcakes behind it on a cutting board.

    Fast, crave-worthy snacks that hit your protein goals (without tracking or extra cooking time).

    Promotion image with an e-book in front and two hands holding it with pages behind it.
    Grab the eBook
    Vanilla protein cupcake with frosting and sprinkles on a blue cupcake liner with more cupcakes behind it.

    Vanilla Protein Cupcakes (Gluten-free)

    Shelby Stover
    Indulge your sweet tooth with these protein cupcakes! Vanilla in flavor and naturally dairy-free, these cupcakes are soft, light, and the perfect way to treat yourself.
    5 from 32 votes
    Print Recipe Pin Recipe
    Prep Time 5 minutes mins
    Cook Time 25 minutes mins
    30 minutes mins
    Total Time 1 hour hr
    Course Dessert
    Cuisine American
    Servings 11
    Calories 203 kcal

    Video

    Equipment

    • Silicone muffin liners
    • Measruing cups and spoons

    Ingredients
      

    • 1.25 cups 1:1 Gluten-free baking flour
    • ¾ cup Collagen powder
    • 1 Egg
    • 1 teaspoon Baking powder
    • ½ cup Sugar
    • 2 tbs Sugar
    • 3 tbs Avocado oil
    • ¾ cup Dairy-free milk
    • ½ tb Vanilla extract
    • ⅛ cup Sprinkles

    Instructions
     

    • Preheat the oven to 350 degrees Fahrenheit.
    • In a large bowl, combine all the dry ingredients (except the sprinkles) and mix well.
    • Add in the wet ingredients one by one and mix until no clumps remain.
    • Line a muffin tray and portion out the batter.
    • Bake for 25 minutes and let cool fully before icing.

    Notes

    You do need both ½ cup and 2 tbs of sugar. They're listed that way to make the nutritional information as accurate as possible.
    Any sugar will work for the cupcakes, I personally use coconut sugar or cane sugar.
    You cannot use chocolate protein powder for these collagen cupcakes. It will absorb too much liquid and the cupcakes will come out funky.
    The batter makes either 12 really small cupcakes or 11 normal-size ones.
    Make sure you use cupcake liners to save your sanity, we use silicone ones the most.
    You can top the protein cupcakes with protein buttercream icing for a smooth, indulgent feel.
    However, cream cheese frosting or adding a double chocolate dairy-free frosting on top works too.
    Make sure to let them cool completely before icing them though.
    If you truly want to make these into chocolate protein cupcakes, add 1-2 teaspoon of cocoa powder to the dry ingredients.
    Disclaimer:

    Nutrition values are estimates only, using online calculators. Please verify using your own data"

    Nutrition

    Calories: 203kcalCarbohydrates: 24gProtein: 17gFat: 5gSaturated Fat: 1gPolyunsaturated Fat: 1gMonounsaturated Fat: 3gTrans Fat: 0.002gCholesterol: 15mgSodium: 63mgPotassium: 66mgFiber: 1gSugar: 14gVitamin A: 85IUVitamin C: 1mgCalcium: 50mgIron: 1mg
    Keyword collagen recipe, dairy free cupcakes
    Have You Tried This Recipe?Please leave a star rating and comment below. Mention @fitasamamabear or tag #fitasamamabear!

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      Dairy-Free Blackberry Popsicles
    • A bowl of cherry crisp with a scoop of ice cream.
      Gluten-Free Cherry Crisp
    • Peanut butter chocolate date bark on top of a wooden board.
      Date Bark Recipe [Dairy-Free]
    • Chocolate cookie being dipped into a bowl of homemade protein cookie butter.
      Homemade Protein Cookie Butter

    Comments

    1. Liz says

      February 27, 2023 at 9:49 am

      5 stars
      This is the best way to satisfy my sweet tooth in a healthy way! So yummy!

      Reply
      • fitasamamabear says

        March 01, 2023 at 4:05 pm

        Right?! Cupcakes are a staple lol

        Reply
    2. Sandi says

      February 27, 2023 at 11:42 am

      5 stars
      I absolutely love the added protein. It helped prevent a lot of sugar buzzed kids at our party.

      Reply
      • fitasamamabear says

        March 01, 2023 at 4:06 pm

        Omg yes. Lol nice to curb that "high" a little bit eh?

        Reply
    3. Shruthi says

      February 27, 2023 at 11:49 am

      5 stars
      As a vegetarian, I've been trying to increase my protein intake and I realize I didn't have to just make protein shakes all the time - loved making a batch of these and munching on them as a snack instead of my usual muffins! So delicious.

      Reply
      • fitasamamabear says

        March 01, 2023 at 4:06 pm

        Protein shakes are great... but they get boring! Glad I can give you a few more sweet options 😉

        Reply
    4. Gina says

      February 27, 2023 at 12:43 pm

      5 stars
      Love the added collagen to help tame the sugar spike you'd typically get from a traditional cupcake. These are such a great way to indulge!

      Reply
      • fitasamamabear says

        March 01, 2023 at 4:06 pm

        Exactly! It's nice to curb the "high" a bit.

        Reply
    5. GRETA says

      February 27, 2023 at 12:54 pm

      5 stars
      I loooove how it came out. So delicious and easy to make. Highly Recommend.

      Reply
      • fitasamamabear says

        March 01, 2023 at 4:07 pm

        Glad you loved them!

        Reply
    6. Sharon says

      June 07, 2023 at 1:19 pm

      5 stars
      Loved 'em! And it wasn't even my birthday. Don't tell anyone! Haha. I was searching for collagen cupcakes and found myself here. These are a really tasty way to get that protein. Thanks!

      Reply
      • fitasamamabear says

        June 08, 2023 at 2:30 pm

        Haha that's amazing that you stumbled on the site, thanks for clicking through! really happy you loved these!

        Reply
    7. Addison says

      June 07, 2023 at 1:50 pm

      5 stars
      These cupcakes were so soft! I loved that they are higher in protein and gluten free.

      Reply
      • fitasamamabear says

        June 08, 2023 at 2:31 pm

        Definitely a huge win, glad you liked them!

        Reply
    8. Rebecca says

      June 07, 2023 at 2:29 pm

      5 stars
      It's nobody's birthday around here, but we are always craving birthday cake so I gave these cupcakes a whirl. SO good!!! They absolutely satisfied our craving for a treat without giving us anything to feel guilty about.

      Reply
      • fitasamamabear says

        June 08, 2023 at 2:31 pm

        Haha you and me both! Glad you enjoyed them! We devour them lol

        Reply
    9. Jessica says

      June 07, 2023 at 2:42 pm

      5 stars
      I never want my kids to feel deprived on special occasions, but I just can't stand the idea of giving them "empty" foods. They love the taste of these protein cupcakes, and I love feeling like I've snuck some substance into their treats. Win win!

      Reply
      • fitasamamabear says

        June 08, 2023 at 2:31 pm

        Omg this sums me up perfectly. It's so nice to be able to hand them something that looks indulgent and similar to other things but you can feel GOOD about!

        Reply
    10. Elizabeth S says

      June 07, 2023 at 4:12 pm

      5 stars
      I made these for my best friend's birthday and she absolutely loved them. The cupcake was moist, tender, and had the perfect amount of flavor. She said she would make these over and over again!

      Reply
      • fitasamamabear says

        June 08, 2023 at 2:32 pm

        Aw, this makes my day. Thanks for giving them a go!

        Reply
    11. Yennefer says

      December 11, 2023 at 8:44 pm

      5 stars
      Just followed the recipe to the tee and I loved how they turned out. They were soft, moist and really yummy.

      Reply
      • fitasamamabear says

        December 14, 2023 at 2:34 pm

        Happy to hear it!

        Reply
    12. Krista says

      December 11, 2023 at 10:16 pm

      5 stars
      These cupcakes are moist and fluffy just like traditional ones. I'm making another batch for a friend's birthday!

      Reply
      • fitasamamabear says

        December 14, 2023 at 2:34 pm

        Wahoo! You're a good friend lol

        Reply
    13. Nikki says

      December 12, 2023 at 1:58 am

      5 stars
      They turned out soft and light. Love that they are healthy. Not worrying of having more than 1 piece specially on your birthday.

      Reply
      • fitasamamabear says

        December 14, 2023 at 2:34 pm

        Exactly!

        Reply
    14. Minnie says

      December 12, 2023 at 7:21 am

      Love the extra nutrition you snuck in there while everyone was busy celebrating and eating a delicious cupcake 😉 So smart!

      Reply
      • fitasamamabear says

        December 14, 2023 at 2:34 pm

        Haha gotta get it in somehow!

        Reply
    15. Jem says

      December 12, 2023 at 3:05 pm

      5 stars
      So tasty! And I love the added benefit of protein and less sugar. The kids loved them so they are a keeper in my book.

      Reply
      • fitasamamabear says

        December 14, 2023 at 2:34 pm

        Right?! And such an easy twist.

        Reply
    16. Kim says

      April 08, 2024 at 11:53 am

      5 stars
      Yes please!

      Reply
      • fitasamamabear says

        April 10, 2024 at 5:00 pm

        Haha.

        Reply
    17. Marie says

      April 12, 2024 at 12:46 pm

      5 stars
      I swapped out the cane sugar for coconut palm sugar and it still worked. The cupcakes turned out moist and delicious, with just the right amount of sweetness. Plus, it's a bit of a healthier option, which is always a win in my book!

      Reply
      • fitasamamabear says

        April 16, 2024 at 7:57 am

        Happy you loved them! Always nice to have a treat!

        Reply
    18. Renee says

      April 12, 2024 at 1:43 pm

      5 stars
      These cupcakes are fantastic! Moist and fluffy, with a lovely hint of vanilla. Plus, the colorful sprinkles add a fun touch. Healthy too! They were perfect at our mini party. Everyone loved them.

      Reply
      • fitasamamabear says

        April 16, 2024 at 7:57 am

        Glad you enjoyed them!

        Reply
    19. Laura K says

      April 12, 2024 at 2:19 pm

      5 stars
      Love these. Made them for my nephew who is FG and he and his friends loved them.

      Reply
      • fitasamamabear says

        April 16, 2024 at 7:57 am

        Ahh amazing!!

        Reply
    20. Gretchen says

      April 13, 2024 at 8:21 pm

      5 stars
      I had never thought about adding collagen powder to my cupcakes. I add it to my coffee every morning, but after seeing this recipe, I decided to make cupcakes. I think it makes the texture better, plus the protein is hard to beat.

      Reply
      • fitasamamabear says

        April 16, 2024 at 7:58 am

        Collagen powder is the best haha it works in everything!!

        Reply
    21. Jean says

      April 14, 2024 at 2:01 pm

      5 stars
      These are so cute and I LOVE that they have all that extra protein thrown in. Planning on making these again for an end of school party for my kids. Thanks for the great recipe!

      Reply
      • fitasamamabear says

        April 16, 2024 at 7:58 am

        Right?! Such an easy way to boost intake a bit.

        Reply
    5 from 32 votes (12 ratings without comment)

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    Welcome!

    I'm Shelby, a Certified Strength & Nutrition Coach who has spent the last 10 years helping women feel more comfortable in their skin though home strength training and healthy food- no diets, no shortcuts

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