Preheat oven to 350°F. Lightly grease a 9×13 baking dish.
Add the oats, chia seeds, flaxseed, and brown sugar to a large mixing bowl. If you’re adding protein powder, mix it in now.
I often use a kitchen scale to measure ingredients directly into the bowl to cut down on dishes. Please see ingredient weights above.
Add Greek yogurt, applesauce, milk, eggs, cinnamon, cloves, and vanilla to the dry ingredients. Mix everything together in the same bowl. Add chopped apple to the mixture and give it a final stir.
Pour into the baking dish and spread evenly. Add toppings, if using.
Cover with foil and bake for 20 minutes. Remove foil and bake for another 15-20 minutes, until set.
Let cool for 10–15 minutes if eating immediately. Cool completely before storing in the fridge.