Blend the egg mixture – In a blender, combine eggs, cottage cheese, salt, and pepper. Blend on high for 20–30 seconds until smooth.
Prepare the muffin cups – Place silicone muffin cups in the air fryer basket. Evenly distribute the cheese, spinach, onion, and any optional mix-ins.
Fill the cups – Pour the blended egg mixture into each muffin cup, filling about ¾ of the way full. Stir gently to combine mix-ins.
Cook in the air fryer – Set the air fryer to 290°F (145°C) and air fry for 12–15 minutes until puffed up and set.
Cool and serve – Let the egg bites cool for a minute before removing them from the cups. Enjoy immediately or store for later.