Preheat oven to 350°F and line a 12-cup muffin tin with liners.
In a medium bowl, whisk together flour, protein powder, baking powder, baking soda, cinnamon, nutmeg, and salt.
In another bowl, whisk eggs, cottage cheese, apple butter, maple syrup, melted butter, and vanilla.
Add dry ingredients to wet and stir until just combined. Do not overmix.
Divide batter evenly into muffin cups.
For streusel, mix flour, sugar, cinnamon, and salt. Cut in cold butter and egg with a fork or your fingers until large crumbs form. Sprinkle generously over muffin batter.
Bake 20–22 minutes, until golden and a toothpick comes out clean.
Cool slightly before serving.