Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with liners or spray with nonstick spray.
In a large bowl, whisk together flour, protein powder, baking powder, baking soda, and salt.
In a separate bowl, whisk eggs, Greek yogurt, honey, milk, and vanilla until smooth.
Pour wet ingredients into dry ingredients and stir until just combined (do not overmix).
Gently fold in blueberries.
Divide batter evenly among muffin cups (about 3/4 full).
Bake for 18–22 minutes, or until a toothpick inserted in the center comes out clean.
Cool muffins in the pan for 5 minutes, then transfer to a wire rack to cool completely.