Preheat the oven to 180°C, gas mark 4.
Squeeze out all the extra liquid from the grated courgette.
Quarter the cherry tomatoes and place them in a bowl with the grated courgette, sliced onion, baby spinach and 1 cup of the cheese. Season to taste with salt and pepper.
In a separate bowl, whisk the eggs and milk and season well.
Pour the egg mixture over the vegetables and stir to combine. (You can stop here and leave the mixture covered in the fridge overnight, ready to bake in the morning, or continue and reheat the baked frittatas in the morning.)
Butter the sides of the muffin tin and fill ¾ of each cup with mixture.
Top with the leftover cheese.
Bake for 25-30 minutes, until the egg is set.
Let the frittatas cool before removing from the muffin pan and store them in an airtight container in the fridge.
To reheat, warm the frittatas slightly in a hot oven before serving. Serve with toasted protein bread and garnish with micro greens.