Heat the oven to 350°F. Grease a 12-cup muffin tin very generously, including the top surface, or use silicone liners.
Heat the olive oil in a skillet over medium-high heat. Cook the bell pepper for 3 minutes, then add the spinach and cook until fully wilted and the liquid has evaporated, about 2 minutes more. Spread on a plate to cool.
Whisk the eggs, milk, salt, and pepper together in a large bowl or measuring cup with a spout until well combined and slightly frothy.
Divide the cooled vegetables, green onions, and cheese among the muffin cups. Pour the egg mixture over, filling each cup about three-quarters full.
Bake 20 to 22 minutes, until the centers are just set and barely jiggle. Cool in the pan for 5 minutes, then run a knife around the edges and lift them out.