Preheat oven to 350°F. Generously spray a 12-cup muffin tin with cooking spray or line with silicone muffin liners.
In a large mixing bowl, whisk together eggs, milk, salt, pepper, and garlic powder until well combined and slightly frothy.
Add shredded cheese, bell peppers, spinach, onion, bacon, and cherry tomatoes to the egg mixture. Stir with a wooden spoon to distribute evenly.
Using a ladle or measuring cup, pour egg mixture into prepared muffin cups, filling each about 3/4 full. The mixture will puff up slightly during baking.
Tap the muffin tin gently on the cutting board to release any air bubbles.
Bake for 18-22 minutes until eggs are set in the center and tops are lightly golden. A toothpick inserted in the center should come out clean.
Remove from oven and let cool in the pan for 5 minutes, then run a knife around edges and transfer muffins to a wire rack to cool completely.
Once cooled, store in meal prep containers or zip-top bags. Refrigerate for up to 5 days or freeze for up to 3 months.
To reheat from fridge: Microwave 1 muffin for 30-45 seconds. To reheat from frozen: Microwave for 60-90 seconds or until heated through.