Preheat the oven to 300°F and coat a 12-cup muffin pan with nonstick spray.
Combine the eggs, cottage cheese, salt, and pepper in a blender. Blend on low for about 20 seconds, then increase to medium for another 10 seconds, until smooth.
Divide the egg mixture among the muffin cups, filling each about three-quarters full.
Top each cup with a portion of the diced bell pepper, onion, and chopped spinach, then stir gently to work the vegetables into the mixture.
Bake for about 20 minutes. The tops will rise above the pan while baking and settle as they cool.
Let the egg bites rest in the pan for 5 minutes, then transfer them to a rack to finish cooling.
To freeze, cool completely and freeze the egg bites on a baking sheet without touching for about 2 hours. Transfer to a freezer bag or airtight container and freeze for up to 3 months.