Preheat your oven to 350°F (175°C). This step is crucial to ensure your muffins bake evenly and rise beautifully.
Grease your muffin tin with the extra-virgin olive oil. This will prevent the muffins from sticking and make for easy removal once they’re baked.
In a mixing bowl, combine the 5 free-range eggs and 2 tablespoons of fresh whole milk. Whisk them together until the mixture is smooth and slightly frothy.
Fold in the finely cubed courgette, yellow pepper, red pepper, and chopped shallots into the egg mixture. Season with salt and pepper to taste, stirring everything together until well combined.
Pour the egg and vegetable mixture evenly into the greased muffin tin. Fill each cup about ¾ of the way full to allow for rising.
Place the muffin tin in the preheated oven and bake for about 20-25 minutes, or until the muffins are set and lightly golden on top. You can test for doneness by inserting a toothpick into the center of a muffin; it should come out clean.
Once baked, remove the muffin tin from the oven and let the muffins cool for a few minutes before gently removing them. Serve warm, or let them cool completely before storing them in an airtight container.