Preheat oven to 350 degrees F. Use cooking oil to grease a nonstick muffin pan and set aside.
While oven is preheating, heat the oil in a large nonstick skillet over medium-high heat. Sauté onions for 5 minutes, until soft; add bell peppers, tomato and salt, and sauté for another 3 to 4 minutes. If using sausage, then add along with bell peppers and tomatoes and sauté for another 5 to 7 minutes.
Add spinach and cook until wilted, about 1 minute more. Set aside.
In a large bowl, whisk the eggs, milk, flour, cheese, salt and pepper until well combined.
Portion out the vegetable (and sausage) mixture into 12 muffin wells. Pour the egg mixture on top, and bake for 25 to 30 minutes until firm.