Preheat and prep: Heat oven to 350°F (175°C).
Line a 12-cup muffin tin with liners or lightly grease with oil.
Make oat flour (if needed): Blend rolled oats in a blender until very fine. You’ll need about 2 cups of oat flour (start with roughly 2 1/4 cups oats).
Whisk dry ingredients: In a large bowl, combine 2 cups oat flour, 1/2 cup protein powder, 1 1/2 teaspoons baking powder, 1/2 teaspoon baking soda, 1 1/2 teaspoons cinnamon, a pinch of nutmeg, and 1/4 teaspoon salt.
Stir wet ingredients: In another bowl, whisk 2 large eggs, 3/4 cup Greek yogurt, 1/2 cup unsweetened applesauce, 1/3 cup maple syrup, 2 teaspoons vanilla, and 3 tablespoons oil until smooth.
Fold together: Pour the wet mixture into the dry bowl. Stir gently until just combined.
The batter should be thick but scoopable.
Add apples: Peel (optional), core, and finely dice 1 1/2 cups apples. Fold them into the batter. If using nuts or raisins, add up to 1/2 cup now.
Portion: Divide batter evenly among the 12 muffin cups.
For a bakery-style dome, fill almost to the top; for standard size, fill about 3/4 full.
Optional topping: Sprinkle a few oats, a pinch of cinnamon sugar, or chopped nuts on each muffin.
Bake: Bake 16–20 minutes, or until the tops spring back and a toothpick comes out with a few moist crumbs. Don’t overbake—protein muffins can dry out quickly.
Cool: Let muffins rest in the pan for 5 minutes, then transfer to a rack to cool completely. This helps them set and stay moist.