Preheat your oven to 350°F (175°C).
In a large mixing bowl, whisk together the eggs, milk, Italian seasoning, salt, and black pepper until smooth.
Stir in the Cheddar cheese, goat cheese, chopped squash, spinach, and onion.
Generously coat a 12-cup muffin pan with non-stick cooking spray.
Evenly divide the egg mixture among the muffin cups, filling each about three-quarters full.
Top each cup with a few diced cherry tomatoes.
Bake the Mini Vegetable Frittatas for 20–22 minutes, or until the centers are fully set and lightly golden.
Allow the frittatas to cool for about 5 minutes before gently loosening them with a small knife or spatula.
Serve warm or let cool completely for meal prep.