Rinse the quinoa thoroughly and cook with water or broth according to package directions until fluffy. Let cool slightly.
Grate the zucchini, sprinkle with salt, and let rest for 10–15 minutes. Squeeze out as much moisture as possible using a clean kitchen towel.
Brown the ground beef in a skillet over medium-high heat until fully cooked. Drain excess fat and allow it to cool slightly.
In a large mixing bowl, combine cooked quinoa, zucchini, onion, garlic, cooked beef, eggs, 1 cup of shredded cheese, broth or milk, oregano, basil, red pepper flakes, salt, and pepper.
Stir everything together until evenly combined.
Preheat the oven to 375°F (190°C). Grease a 9×13-inch baking dish.
Spread the Healthy Quinoa Zucchini Bake mixture evenly into the baking dish.
Sprinkle the remaining cheese over the top.
Cover loosely with foil and bake for 30 minutes.
Remove the foil and bake another 15–20 minutes until golden brown and bubbly.
Let the casserole rest for 10–15 minutes before slicing and serving.