Spray a large non-stick skillet with cooking spray and heat over medium-high.
Whisk eggs, milk, vanilla, 1 teaspoon cinnamon, and 1 teaspoon nutmeg in a shallow dish.
Dip bread in egg mixture, turning to coat both sides, then place onto hot skillet.
Cook French toast until both sides are golden and egg is cooked through.
Meanwhile, slice or chop apples.
Place apples in a microwave safe dish. Stir in water and remaining spices, then cover and microwave on high for 1 minute.
Stir apples, return cover, and microwave for another 2-3 minutes or until soft.
Top French toast with warmed apples before serving.