Lightly grease six silicone muffin liners or a small air fryer-safe muffin tin with cooking spray. This ensures the eggs won’t stick and makes cleanup much easier later.
In a medium mixing bowl, crack the eggs and add the milk, salt, and black pepper. Whisk vigorously until the yolks and whites are fully combined and the mixture is slightly frothy.
Place an even amount of diced bell peppers, chopped spinach, and shredded cheese into the bottom of each prepared muffin liner. This ensures every bite is filled with flavor.
Carefully pour the egg mixture into each liner over the fillings. Fill them about 3/4 of the way full, as the eggs will puff up significantly while cooking in the air fryer.
Place the liners into the air fryer basket. Set the air fryer to 300°F (150°C) and cook for 12 to 15 minutes. The muffins are done when the centers are set and no longer jiggly.
Allow the muffins to sit in the air fryer for 2 minutes after cooking. Carefully remove them and let them cool for another few minutes before popping them out of the liners to serve.