Heat the oven to 350°F. Butter a 9-by-13-inch baking dish and toast the muffin pieces on a sheet pan for 8 minutes.
Cook the bacon in a skillet over medium heat for 10 to 12 minutes until crisp. Drain on paper towels.
Spread the muffins, bacon, tomatoes and cheddar in the baking dish. Whisk the eggs, milk, salt and pepper and pour evenly over the filling.
Press down gently and let stand for 10 minutes. Bake for 30 to 35 minutes, until the center custard reaches 160°F and the edges puff.
Rest for 10 minutes before cutting; use a thin spatula to lift the muffin base with each square.