Preheat oven to 375° and line a 12 count muffin tin.
In a medium mixing bowl, mix together the flour, protein powder, baking powder, and baking soda. Set aside.
In a separate bowl, whisk together plain Greek yogurt, sugar, oil, milk, eggs, orange juice, zest, and vanilla extract. Whisk until no lumps remain and everything is smooth.
Add the dry ingredients and stir until almost combined. Fold in ¾ cup of the chopped cranberries until just combined.
Divide the batter evenly between 12 muffins, then top evenly with the remaining ¼ cup chopped cranberries. Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted in the center comes out clean. Allow to cool, then serve!