Preheat your air fryer to 300°F (150°C) for 3 minutes if required.
Lightly spray the inside of each silicone mold with cooking spray, coating the sides all the way to the rim.
In a large bowl, whisk the eggs, milk, salt, and pepper vigorously for 30-45 seconds until pale and frothy.
Add the bell pepper, spinach, bacon, onion, and half the cheese to the egg mixture and stir until evenly distributed.
Pour the egg mixture evenly into the 6 greased molds, filling each about 3/4 full.
Place the filled molds in the air fryer basket, leaving space between them for airflow. Air fry at 300°F (150°C) for 10-12 minutes.
Check doneness with a toothpick. If it comes out clean, the cups are done. If still wet, cook for 1-2 more minutes.
Sprinkle the remaining cheese on top and increase heat to 400°F (200°C) for 1-2 minutes until melted and golden.
Carefully remove the molds using tongs or mitts, let rest for 1-2 minutes, then pop the egg cups out and serve.