Spray a 12-cup muffin tin with cooking spray and preheat the oven to 350 F.
Dice the bacon and put it in a large skillet. Place the pan over medium heat and cook, stirring occasionally until just crisp, about 6 minutes. Use a slotted spoon or spatula to remove the bacon pieces to paper towels to drain.
Remove all but 1 to 2 teaspoons of the drippings and add the spinach to the pan. Cook for about 1 to 2 minutes, or just until wilted. Set aside.
In a large bowl, whisk the eggs with half-and-half, salt, pepper, and nutmeg, then add the shredded cheese and whisk until well blended.
Add the diced tomatoes and the cooked bacon and spinach.
Divide the mixture evenly among the 12 muffin cups.
Bake the egg bites until they are puffed up and lightly browned, about 16 to 18 minutes.
Remove the pan to a rack and cool slightly. To remove the egg bites from the pan, run a knife or spatula around the edge of each one and lift them out of the pan.