October 19, 2016


National Chocolate Cupcake Day got me craving a rich chocolate cupcake piled high with indulgent chocolate frosting… so I made these Chocolate Protein Cupcakes! These cupcakes may taste super decadent, but each cupcake has less than 5 grams of fat and just 3 grams of sugar! Not to mention, they’re high in protein for the perfect post-workout or anytime snack. Being a raving chocoholic, I made these cupcakes full of intense chocolate flavor! If you find them too rich, maybe try using a couple tablespoons less cacao powder and maybe less sweetener 😉

Don’t do dairy? Try my Chocolate Collagen Protein Cupcakes!


What protein powder works best?

I used Quest Protein Powder in Chocolate Milkshake for this cake. You can use whatever you have on hand, but some work better than others. Whey blends (like Quest) combining whey isolate, casein, and milk protein work best for baking! Whey concentrate would be a close second. Whey isolates are the absolute worst for baking. They tend to make baked goods come out spongey or dry (unless you use very little).

You can try substituting vegan protein powder in this recipe, though I haven’t tested it. In my experience, you may need extra liquid to thin out the batter if using a plant-based protein powder 😉


Flour substitutions

I used coconut flour to keep these cupcakes low in carbs, but you can also use twice as much (one half cup) gluten-free baking flour. You can also use half a cup of all-purpose flour, brown rice flour, cake flour, sweet white sorghum flour, or any other fine flour. This will result in a fluffier, more tender cupcake (coconut flour can be a little coarse).


Sweetener substitutions

To add sweetness without any calories, I used my favorite organic stevia blend that’s twice as sweet as sugar with no bitter aftertaste. If your stevia tastes bitter, it’s probably cheap! I generally avoid store brand stevia and stick to either Truvia or Pyure.

Feel free to substitute the stevia blend for twice as much (two thirds cup) baking stevia, granulated erythritol, monk fruit blend, or a granulated sugar like coconut sugar. If using stevia extract or drops, please refer to the brand-specific conversion chart.


Other substitutions

These cupcakes are incredibly moist thanks to the combination of 100% pure canned pumpkin, unsweetened applesauce, nonfat plain Greek yogurt, and a tiny bit of avocado oil. Combining these together prevents any one flavor for coming through too strong (especially the Greek yogurt or unsweetened applesauce). However, you can substitute the applesauce and Greek yogurt for more pumpkin, since it’s pretty neutral in flavor and the rich cacao overpowers it.

A little brewed coffee enhances the cacao flavor, but feel free to substitute unsweetened almond milk or whatever milk you have on hand!


Chocolate protein frosting

The creamy dreamy frosting is a combo of Greek cream cheese, Quest Protein Powder, Special Dark Cocoa, stevia blend , and vanilla extract. Feel free to use whatever chocolate protein powder you have on hand, or use your sweetener of choice to taste. If you can’t find Greek cream cheese, you can substitute whipped cream cheese, reduced fat cream cheese, or Neufchatel cheese. All of these alternatives will be slightly lower in protein, reducing the protein per cupcake by 1-2 grams.

Now, enough from me… here’s the recipe for these Chocolate Protein Cupcakes! Please rate and comment below if you try this recipe to let me know whatcha think 🙂

This post contains affiliate links.

Chocolate Protein Cupcakes

These Chocolate Protein Cupcakes are moist and decadent with a delicious chocolate protein frosting! Low carb, low sugar, high protein, and gluten free.
Course Dessert
Prep Time 20 minutes
Cook Time 20 minutes
Servings 10 cupcakes
Calories 123kcal



  • 1/2 cup (60g) chocolate whey blend protein powder I used Quest brand in Chocolate Milkshake
  • 6 tbsp. calorie-free sweetener* I used one that's twice as sweet as sugar
  • 6 tbsp. special dark unsweetened cocoa aka Dutch process cocoa
  • 1/4 cup coconut flour* or 1/2 cup gluten-free baking flour
  • 3/4 tsp. baking powder
  • 1/4 tsp. salt optional
  • 1/4 cup (2 large) egg whites
  • 1/2 cup 100% pure canned pumpkin
  • 1/4 cup unsweetened applesauce* or more pumpkin
  • 1/4 cup nonfat plain Greek yogurt* or more pumpkin
  • 1/4 cup brewed coffee* or water or milk of choice
  • 1 tbsp. vegetable oil or melted coconut oil
  • 1/2 tsp. vanilla extract optional


  • 6 oz. Greek cream cheese* or Neufchatel, reduced fat or whipped cream cheese
  • 1/3 cup (40g) chocolate whey blend protein powder I used Quest brand in Chocolate Milkshake
  • 1/4 cup calorie-free sweetener* I used one that's twice as sweet as sugar
  • 3 tbsp. special dark unsweetened cocoa or Dutch process cocoa
  • 3 tbsp. unsweetened almond milk or milk of choice
  • 1/4 tsp. vanilla extract


  • Preheat oven to 350 degrees F.
  • Whisk together dry ingredients (through salt) in a medium mixing bowl.
  • Add wet ingredients (through vanilla), then mix into dry ingredients until combined.
  • Line nine wells of a muffin pan with silicone, paper or foil cupcake liners and spray the insides with cooking spray. Alternatively, spray the insides of a nonstick muffin pan with cooking spray and omit liners.
  • Divide cupcake batter between prepared wells and bake for 17-22 minutes, until barely set in the center.
  • While cupcakes cool, blend together frosting ingredients until smooth.
  • Spoon frosting into a piping bag or sealed baggie with one corner cut off to frost cupcakes.
  • Decorate frosted cupcakes with sprinkles (if desired) and enjoy!
  • Cupcakes will keep in an airtight container in the fridge up to one week or in the freezer up to one month. Thaw at room temp before eating.


Calories (per cupcake with frosting): 123kcal, Fat: 4.7g, Sat fat: 2.3g, Carbs: 9g, Fiber: 4g, Sugar: 3g, Protein: 13g, Sodium: 220mg

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