Preheat the oven to 350°F (175°C). Grease a 9x13-inch baking dish with cooking spray or olive oil.
In a skillet, heat the olive oil over medium heat. Add the diced onion and red bell pepper. Sauté until the vegetables are tender, about 5 minutes. Add the chopped spinach and cook for an additional 2 minutes until wilted. Remove from heat and set aside.
In a large mixing bowl, whisk together the eggs and milk until well combined.
Add the cooked vegetable mixture, diced ham or turkey sausage, diced bread, shredded cheddar cheese, dried thyme, salt, and pepper to the egg mixture. Mix everything together until the ingredients are evenly distributed.
Pour the mixture into the prepared baking dish, spreading it out evenly.
Bake in the preheated oven for 25-30 minutes, or until the casserole is set in the center and the top is lightly golden.
Once cooked, remove the casserole from the oven and let it cool slightly before slicing.
If you plan to make this casserole ahead of time, allow it to cool completely before covering and refrigerating. To reheat, simply place individual portions in the microwave or oven until heated through.
Serve the healthy Make-Ahead Breakfast Casserole warm, either on its own or with a side of fresh fruit or yogurt.