01 - Preheat oven to 350°F. Grease a 12-cup muffin tin thoroughly or line with paper liners for easy removal.
02 - Heat olive oil in a skillet over medium heat. Add diced onion and cook 2-3 minutes until softened. Add minced garlic and chopped spinach; cook until spinach wilts completely, about 2 minutes. Remove from heat.
03 - Crack eggs into a large mixing bowl. Add milk, salt, pepper, and nutmeg if using. Whisk vigorously until fully combined and slightly frothy.
04 - Add the cooked spinach mixture to the egg bowl. Fold in crumbled feta cheese and shredded cheese if using. Mix gently to distribute evenly without deflating the eggs.
05 - Divide the egg and vegetable mixture evenly among the 12 prepared muffin cups. Fill each cup about three-quarters full, leaving room for rising during baking.
06 - Bake at 350°F for 18-20 minutes until the muffins are set throughout and lightly golden on top. A toothpick inserted in the center should come out clean.
07 - Let muffins cool in the tin for 5 minutes before removing. Run a thin knife around the edges if needed. Serve warm or at room temperature.