Preheat your oven to 375°F (190°C) and lightly grease a small oven-safe baking dish with the extra virgin olive oil.
In a medium mixing bowl, combine the low-fat cottage cheese, chopped chives, fresh dill, sea salt, and black pepper.
Roughly chop the baby spinach and fold it into the cottage cheese mixture until evenly distributed.
Transfer the cottage cheese and spinach mixture into the prepared baking dish, smoothing the top with a spatula.
Using the back of a spoon, create three small wells in the mixture to hold the eggs.
Carefully crack one egg into each well, ensuring the yolks remain intact.
Sprinkle the grated parmesan cheese over the top of the eggs and cottage cheese.
Bake in the center of the oven for 15 to 18 minutes, or until the egg whites are completely opaque and set, while the yolks remain slightly soft.
Remove from the oven and let the dish rest for 2 minutes before serving warm.