March 01, 2016 1 Comment


I haven’t done a lemon recipe for awhile so these Lemon Protein Cupcakes are for all you lemon lovers out there! Think fluffy sweet vanilla cake with just the right amount of fresh lemon flavor topped with cream cheese frosting. Not too sweet, not too tart. Even “non-healthy” eaters love them! My dad is the epitome of a “non-healthy” eater in that he grew up with my German grandmother’s baking (she makes the most incredible dream bars!). Anyway, yesterday he stopped by just as these were coming out of the oven, so of course, he got to have one. His first response was “Mmmmmm!” followed by “I need to come by more often!” Boy, was he shocked to learn these cupcakes are high in protein, low carb, low fat and low sugar 😉

Protein recommendations

To up the protein in these beauties, I used Quest Protein Powder in Vanilla Milkshake. 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

To keep the carbs low, I opted for a combination of gluten-free baking flour and coconut flour. You can swap the coconut flour out for twice as much gluten-free flour (half a cup) if that’s all you have. You can also use all-purpose flour, brown rice flour, cake flour, fine oat flour, or white sorghum flour. All of these tend to result in fluffy, light baked goods. I would not recommend substituting almond flour (it can be a little mealy), but if you try it, start with 2 cups.

Sweetener substitutions

For just the right amount of sweetness with no bitter aftertaste, I used Pyure Organic Stevia Blend. This sweetener is an organic, calorie-free blend of erythritol and stevia that’s twice as sweet as sugar. If substituting baking stevia, granulated erythritol, granulated monk fruit, or sugar, you’ll need to use twice as much (half a cup).

Other substitutions

The remaining cupcake ingredients are pretty basic: lemon zest and juice, nonfat plain Greek yogurt, unsweetened applesauce, and egg whites. I used two medium lemons for this recipe, so you may need only one large lemon. If you’re allergic to eggs, try a vegan egg substitute! For extra decadence, add a tablespoon of melted coconut oil to the batter (this will of course, increase the fat and total calories).

Cream cheese frosting

The frosting is a simple combo of whipped cream cheese (my favorite for frosting!), nonfat plain Greek yogurt, confectioner’s erythritol (can use powdered sugar), a hint of lemon juice and vanilla extract.

Okay, here’s the recipe for these luscious Lemon Protein Cupcakes! Please leave a comment below if you try them 🙂

This post contains affiliate links.

Lemon Protein Cupcakes

These Lemon Protein Cupcakes combine a fluffy sweet lemon cupcake with cream cheese frosting. Low fat, gluten-free, and less than 100 calories each!
Course Dessert
Prep Time 20 minutes
Cook Time 20 minutes
Servings 9 cupcakes
Calories 98kcal


  • 1/2 cup (60g) vanilla whey blend protein powder I used Quest brand in Vanilla Milkshake
  • 1/4 cup gluten-free baking flour*
  • 1/4 cup coconut flour*
  • 1/4 cup calorie-free sweetener* I used one that's twice as sweet as sugar
  • 3/4 tsp. baking powder
  • 1/4 tsp. salt optional
  • 1/2 cup nonfat plain Greek yogurt
  • 1/2 cup unsweetened applesauce
  • 1/4 cup (2 large) egg whites*
  • 1 tbsp. melted coconut oil* optional
  • 1/4 cup lemon juice
  • 2 tbsp. lemon zest


  • 4 oz. whipped cream cheese
  • 2 oz. nonfat plain Greek yogurt
  • 1/3 cup powdered calorie-free sweetener* I used confectioner's erythritol
  • 1 tsp. lemon juice
  • 1/4 tsp. vanilla extract

*See blog post above for substitutions.


    • Preheat oven to 350 degrees F.
    • Whisk together dry ingredients (through salt) in a medium mixing bowl.
    • Add egg whites, unsweetened applesauce and Greek yogurt (don't mix yet).
    • Zest two lemons using the fine side of a grater. Avoid getting into the bitter pith (white part).
    • Add zest and juice to batter and mix just until no clumps remain.
    • Line nine wells of a muffin pan with paper, foil, or silicone cupcake liners (if using paper, lightly spray the insides with cooking spray for easier removal after baking).
    • Fill each cup almost to the top with batter.
    • Bake for 20-25 minutes until a toothpick or knife inserted in the center comes out clean.
    • While cupcakes cool, mix up your frosting.
    • Spread frosting over cupcakes and enjoy! For fancier cupcakes, use a piping bag or a Ziploc with one corner cut off to frost cupcakes and garnish with lemon zest.
    • Leftover cupcakes will keep in the fridge in an airtight container up to one week.


    Calories (per cupcake with frosting, minus optional ingredients): 98kcal, Fat: 2.2g, Sat fat: 1.4g, Carbs: 9g, Fiber: 2g, Sugar: 4g, Protein: 10g, Sodium: 101mg
    Calories (per cupcake with frosting, including optional ingredients): 112kcal, Fat: 3.7g, Sat fat: 2.6g, Carbs: 9g, Fiber: 2g, Sugar: 4g, Protein: 10g, Sodium: 165mg

    1 Response

    Bella Devine
    Bella Devine

    April 08, 2024

    Your print button for this recipe is broken. Waaaaa!

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