Preheat the oven to 350°F.
In a medium bowl, whisk eggs, salt, & pepper until well combined.
Spray a muffin pan very well with cooking spray, or line with silicone or parchment liners. Divide the red pepper, onion, ham/bacon/sausage, and cheese over 12 wells.
Pour the egg mixture over the cheese mixture.
Bake for 22-25 minutes or until set.
Let rest 3 minutes. Run a butter knife along the edges to release the muffins and remove them from the muffin tin.
Serve warm or let cool completely and refrigerate or freeze.
