Preheat oven to 350 degrees F and spray a muffin pan (12 wells) with a cooking spray and set aside.
Wring all the excess water from the spinach using paper or cloth towel
Heat the oil in a large skillet or wok over medium-high heat. Sauté onions until soft (about 5 minutes), add bell peppers, tomato and salt, and sauté for another 3 to 4 minutes. Add spinach and gentle stir to combine, remove from heat. Set aside.
In a large bowl, whisk eggs, milk, flour, cheese, salt and pepper until well combined.
Portion out the vegetable mixture into each of the muffin wells. Pour the egg mixture on top.
Place in preheated oven and bake for 25 to 30 minutes until firm.