Spray muffin tins with nonstick spray. Dredge with flour and shake off excess to leave thin coating of flour.
Dice chicken ham deli slices and set aside.
Whisk the eggs, milk, pepper, and salt in a large bowl to blend well.
Refrigerate until ready for use.
Sautee onions, sweet pepper and tomato in hot pan until lightly caramelized. Remove from heat, let cool a bit, the add thyme leaves and ham and cheddar cheese and gently mix.
Scoop 1 tbsp of vegetable and ham mixture at the bottom of each muffin tin.
Fill prepared muffin tins with egg mixture until almost to the top.
Bake until the egg mixture puffs and is just set in the center, about 8 to 10 minutes. Let cool a little for about 5 minutes.
Using a rubber spatula or butter knife to loosen the frittatas from the muffin cups and slide the frittatas onto a platter.
Serve immediately with toast, fried ripe plantains or hash browns!