Whisk eggs, almond milk, protein powder, vanilla extract, pumpkin pie spice and pumpkin puree until smooth.
Pre-heat oven to 350 degrees and spray a muffin tin with non-stick cooking spray or arrange 3 jumbo muffin cups on a baking sheet.
Gently dunk bread chunks into egg mixture, completely coating all of the bread. Let bread soak in egg mixture for about 10 minutes, it should absorb almost all of the egg mixture.
Place a layer of bread in the bottom of the muffin cups, then add some apple chunks on top. Layer more bread on top of apples and pour any remaining egg mixture on top.
Bake at 350 degrees for 18-20 minutes (increase to 23-25 minutes if using jumbo muffin cups).
While French toast cups are baking, add remaining apple chunks and maple syrup to a small pan. Add some ground cinnamon if desired. Bring to a boil over medium heat, then lower heat to a simmer for 5-10 minutes until apples are tender.
Pour apple syrup over French toast cups. Mix Greek yogurt and casein protein powder until smooth, then add on top of French toast cups before serving.