Preheat the oven to 350°F (175°C).
In a large skillet, heat olive oil over medium heat. Add diced onion and cook until translucent, about 5 minutes. Stir in the minced garlic and cook for another minute.
Add the fresh spinach to the skillet and cook until wilted, about 3-4 minutes. Remove from heat and allow to cool slightly.
In a large mixing bowl, combine the cottage cheese, mozzarella cheese, Parmesan cheese, eggs, salt, black pepper, red pepper flakes, and nutmeg. Mix until well combined.
Add the cooked spinach mixture to the cheese mixture and stir until evenly distributed.
Pour the spinach and cheese mixture into a greased baking dish and spread it evenly.
Sprinkle breadcrumbs on top for a crunchy texture.
Bake in the preheated oven for about 30 minutes, or until the top is golden brown and the casserole is set.
Remove from the oven and let it cool slightly before serving.