Preheat oven to 375 degrees F. Coat 12 muffin tins with non-stick cooking spray.
In a medium bowl add the eggs and milk and whisk well. Season with salt and pepper, to taste.
Heat a skillet over medium high heat and generously spray with non-stick cooking spray. Add onion and bell pepper and cook for 5-6 minutes until tender and onions are translucent. Add spinach and cook until wilted, about 1 minute. Remove from heat and divide veggies into the prepared muffin tin.
Pour eggs in each cup over the veggies and fill 2/3 of the way full.
Sprinkle with cheese and cooked bacon.
Cook in preheated oven for 12-15 minutes, or until eggs are set.