Preheat oven to 375 degrees F (190 degrees C). Line 12 muffin cups with paper liners.
Whisk oats, quinoa flour, ground flax seed, baking powder, baking soda, 1 scoop protein powder, 2 packets stevia powder, 1 teaspoon cinnamon, and nutmeg together in a bowl. Stir sweet potato, eggs, Greek yogurt, coconut oil, applesauce, and vanilla extract together in a separate bowl; stir in flour mixture until batter is smooth. Spoon batter into the prepared muffin cups.
Bake in the preheated oven until a toothpick inserted in the center comes out clean, about 17 minutes. Cool slightly, about 15 minutes.
Whisk 1/2 scoop protein powder, 2 packets stevia powder, 1 1/2 teaspoons cinnamon, and water together in a bowl, adding more water to thin the glaze. Brush glaze over slightly cooled muffins.
