Preheat the oven to 400°F (200°C).
For individual portions, divide the cherry tomatoes, diced bell pepper, red onion, minced garlic, and feta evenly among four oven-safe ramekins. Drizzle each portion with approximately 1 tablespoon olive oil.
For one large baking dish, add the tomatoes, bell pepper, onion, and garlic to the dish. Place the feta in the center and drizzle the olive oil over the cheese and vegetables.
Combine the oregano, sea salt, thyme, black pepper, and red pepper flakes in a small bowl.
Sprinkle the seasoning mixture evenly over the feta and vegetables.
If using ramekins, arrange them on a rimmed baking sheet for easier handling.
Bake for approximately 25 minutes, until the tomatoes have softened and started to burst and the feta is hot and creamy.
Carefully remove the baking dish from the oven. Stir the feta into the roasted vegetables until creamy and evenly distributed.
Add the chopped baby spinach and stir until incorporated. The residual heat will begin to wilt it.
Make four wells in the feta and vegetable mixture. If using individual ramekins, make one well in each.
Carefully crack one egg into each well.
Return the Baked Feta Eggs Recipe to the oven and bake for approximately 8–12 minutes. The exact cooking time depends on how set you prefer the yolks.
Remove from the oven when the egg whites are fully set and the yolks have reached your preferred consistency.
Sprinkle with chopped fresh basil or chives, if desired.
Serve immediately with warm pita, toasted baguette, or crusty bread.