Preheat the oven to 350°F (175°C). Grease a muffin tin or line with muffin liners.
Heat a skillet over medium heat and cook bacon until crispy. Remove from skillet and drain on paper towels. Crumble the bacon and set aside.
In the same skillet, cook the diced bell peppers until softened, about 5 minutes. Remove from heat.
In a bowl, whisk together the eggs, milk, salt, and pepper.
Divide the crumbled bacon and cooked bell peppers evenly among the muffin cups. Pour the egg mixture over the bacon and bell peppers, filling each cup about 3/4 full.
Sprinkle shredded cheddar cheese on top of each muffin cup.
Bake in the preheated oven for 20-25 minutes, or until the eggs are set and the tops are golden brown.
Remove from the oven and allow to cool slightly before serving.
Enjoy warm or refrigerate for later.