Preheat the oven to 400°F (204°C).
For individual portions, divide the cherry tomatoes, chopped bell pepper, red onion, garlic, and feta evenly among four oven-safe ramekins. Drizzle each portion with olive oil.
Alternatively, place the tomatoes, bell pepper, onion, and garlic in one larger baking dish. Position the feta in the center and drizzle the olive oil over the vegetables and cheese.
In a small bowl, combine the oregano, thyme, salt, black pepper, and red pepper flakes.
Sprinkle the seasoning mixture evenly over the feta and vegetables.
If using ramekins, arrange them on a baking sheet. Bake for approximately 25 minutes, until the tomatoes begin to burst and the vegetables are tender.
Carefully remove the baking dish from the oven. Stir the roasted feta and vegetables together until the cheese creates a creamy coating.
Add the chopped spinach and stir until evenly distributed. The residual heat will begin wilting the spinach.
Create a well in the center of each ramekin. If using one large baking dish, make four evenly spaced wells.
Crack one egg into each well.
Return the Baked Feta Eggs to the oven and bake until the egg whites are set and the yolks reach your preferred consistency, approximately 8–12 minutes. Begin checking early because oven temperatures and baking dishes can affect cooking time.
Remove from the oven and garnish with fresh parsley, sliced green onions, or chopped chives before serving.