01 - Preheat oven to 350°F. Lightly grease a 12-cup muffin tin or line each cavity with paper liners.
02 - In a skillet over medium heat, cook diced onion in a splash of oil until softened and translucent, about 3 to 4 minutes. Add chopped spinach and sauté until wilted, or just warmed if using thawed frozen spinach. Remove skillet from heat and set aside to cool slightly.
03 - In a large mixing bowl, whisk together eggs, ricotta cheese, milk, salt, pepper, and nutmeg until fully combined and smooth.
04 - Stir shredded cheddar, Parmesan cheese, sautéed onion and spinach mixture, and fresh herbs if using into the egg mixture until evenly incorporated.
05 - Divide prepared mixture evenly between muffin cups, filling each cavity about three-quarters full.
06 - Transfer pan to preheated oven and bake for 18 to 22 minutes, or until muffins are just set and tops are lightly golden.
07 - Allow muffins to cool in pan for 5 minutes, then transfer to a wire rack. Serve warm or at room temperature.