Preheat the oven to 400°F.
For individual servings, divide the tomatoes, red bell pepper, red onion, garlic, and feta between four oven-safe ramekins or individual baking dishes. Drizzle 1 tablespoon of olive oil over each dish.
For one large baking dish, add the tomatoes, bell pepper, red onion, and garlic to the dish. Place the feta cheese in the center and drizzle the olive oil over the feta and vegetables.
In a small bowl, combine the dried oregano, sea salt, dried thyme, black pepper, and red pepper flakes.
Sprinkle the seasoning mixture evenly over the feta and vegetables.
Place individual ramekins on a baking sheet, or place the large baking dish directly in the oven. Bake for 25 minutes.
Remove the dish from the oven and stir the roasted vegetables and feta together until the feta is evenly distributed.
Add the chopped spinach and stir until combined and slightly wilted.
Create four wells in the mixture if using one large dish, or one well in the center of each ramekin. Crack an egg into each well.
Return the dish to the oven and bake for about 10 minutes, or until the egg whites are set and the yolks reach your preferred doneness.
Remove from the oven and garnish with chopped fresh basil or chives, if desired.
Serve the Baked Feta Eggs Recipe warm with crusty baguette, toast, or pita for dipping.