Preheat oven to 350. Line a muffin tin with parchment paper liners.
Heat a small skillet over medium high heat and add olive oil.
When oil is hot, add bell peppers and shallots, reduce heat to medium low. Season with salt and pepper.
Saute the pepper and shallot until soft and golden, about 5 minutes. Keep a close eye on it, as the shallot tends to burn quickly.
In the meantime, whisk eggs until scrambled, add salt and pepper to taste.
Spoon the peppers and shallot mixture evenly among the muffin tin liners.
Evenly pour the egg mixture over the pepper shallot mixture, filling each muffin cup about 3/4 full.
Bake in the oven until egg is set and puffy, about 15-20 minutes.
After removing from oven, immediately remove from muffin tin and allow to cool completely on a cooling rack.
Store in the refrigerator for up to five days.