Preheat and prep: Heat your oven to 375°F (190°C). Lightly grease a 9x13-inch baking dish with cooking spray or oil.
Sauté the veggies: Warm the olive oil in a large skillet over medium heat.
Add onion and mushrooms with a pinch of salt. Cook 4–5 minutes until softened and most moisture cooks off.
Add pepper and spinach: Stir in the bell pepper and cook 2 minutes. Add garlic and cook 30 seconds.
Add spinach in batches, stirring until wilted. Remove from heat and let cool slightly.
Whisk the egg mixture: In a large bowl, whisk eggs, cottage cheese (or Greek yogurt), milk, salt, pepper, and smoked paprika. Mix until mostly smooth; small curds from cottage cheese are fine.
Add cheese and vegetables: Fold in half the shredded cheese and the cooked vegetables.
Taste a small spoonful and adjust salt if needed.
Assemble: Pour the mixture into the prepared baking dish. Sprinkle the remaining cheese over the top. Add red pepper flakes if using.
Bake: Place on the center rack and bake 28–35 minutes, until the edges are set and the center barely jiggles.
A knife inserted near the center should come out mostly clean.
Rest and serve: Let the casserole rest 10 minutes before slicing. Garnish with chopped parsley or chives if you like.