Preheat the oven to 350°F.
In a large skillet over medium heat, heat the olive oil.
Sauté the onion and garlic until the onion is slightly translucent, about 5 minutes.
Add the mushrooms, and cook for another 5 to 10 minutes.
Stir in the bell pepper.
Remove the skillet from the heat.
In a medium bowl, whisk the eggs together.
Set aside.
Pour some of the egg mixture into each bacon-lined muffin well, and then spoon the sautéed veggie mixture into each one.
Bake for 25 minutes, or until the eggs are firm, and serve.