Preheat and prep: Heat the oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or grease lightly.
Mix dry ingredients: In a large bowl, whisk 1 cup all-purpose flour, 3/4 cup vanilla protein powder, 1 1/2 teaspoons baking powder, 1/2 teaspoon baking soda, and 1/4 teaspoon salt until well combined.
Whisk wet ingredients: In a separate bowl, whisk 2 large eggs, 1/2 cup Greek yogurt, 1/3 cup sugar (or 1/3 cup maple syrup), 1/3 cup milk, 1/4 cup oil, and 2 teaspoons vanilla extract until smooth.
Combine gently: Pour the wet mixture into the dry. Stir with a spatula just until you don’t see dry streaks. If adding mix-ins, fold in up to 3/4 cup now.
The batter will be thick—avoid overmixing.
Portion: Divide the batter evenly among the 12 cups, filling each about 3/4 full. For bakery-style domes, let the filled pan rest for 5 minutes before baking.
Bake: Place on the middle rack and bake for 15–18 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs.
Cool: Let the muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely. This helps them stay tender and prevents soggy bottoms.
Taste and adjust: Once cool, taste one.
If you prefer a sweeter batch next time, add 1–2 extra tablespoons of sugar or a few chocolate chips.