Preheat your oven to 350°F (175°C). Grease a muffin tin with cooking spray.
In a small skillet, heat a tablespoon of olive oil over medium heat. Add diced peppers and onions, and sauté until they are soft and slightly caramelized, about 5-7 minutes. Set aside to cool.
In a large mixing bowl, whisk together the eggs. Season with salt and pepper to taste.
Divide the sautéed peppers and onions evenly among the muffin cups.
Pour the egg mixture over the vegetables, filling each muffin cup about three-quarters of the way full.
Bake in the preheated oven for 20-25 minutes, or until the egg cups are set and slightly golden on top.
Remove from the oven and allow to cool for a few minutes before serving. Enjoy immediately, or store in an airtight container in the refrigerator for later.