Preheat and prep: Set your oven to 350°F (175°C). Line a 12-cup muffin tin with liners or lightly grease it.
Whisk dry ingredients: In a large bowl, whisk 1 cup vanilla protein powder, 3/4 cup oat flour, 1/2 cup almond flour, 1 1/2 teaspoons baking powder, 1/4 teaspoon baking soda, and 1/4 teaspoon salt.
Mix wet ingredients: In another bowl, whisk 3/4 cup Greek yogurt, 1/2 cup unsweetened applesauce, 1/4 cup neutral oil, 1/2 cup egg whites (or 2 whole eggs), 1 teaspoon vanilla, and 1/3–1/2 cup sugar (adjust to taste). Stir in 1/4 cup milk.
Combine gently: Pour wet into dry.
Stir with a spatula until just combined. The batter should be thick but scoopable. If it’s too thick (crumbly), add 1–2 tablespoons more milk.
Add extras: Fold in up to 1/3 cup of your favorite add-ins—mini chocolate chips, blueberries, or chopped nuts.
Fill the tin: Divide batter evenly among the cups, about 3/4 full.
Smooth the tops lightly.
Bake: Place on the center rack and bake for 14–18 minutes, or until the tops spring back and a toothpick comes out clean or with a few moist crumbs.
Cool: Let cupcakes rest in the pan for 5 minutes, then transfer to a rack to cool completely. This helps set the structure so they don’t crumble.
Optional frosting: Beat 4 ounces softened cream cheese, 1/2 cup Greek yogurt, 1/2–3/4 cup powdered sugar, and 1 teaspoon vanilla until smooth. Chill 15 minutes, then spread or pipe onto cooled cupcakes.