Preheat the oven to 375°F.
Line a baking sheet with parchment and place the bacon on it.
Cook the bacon until crisp, about 15 to 20 minutes.
While the bacon cooks, cook the sausage, breaking it up with a spatula.
Remove the cooked sausage, then cook the onion and spinach until the onion is tender.
Cool the bacon and crumble it.
Reduce the oven temperature to 350°F.
Whisk the eggs with the milk, salt, and pepper in a large bowl.
Grease a muffin tin and divide the sausage, spinach, onion, egg mixture, and most of the bacon among the cups.
Bake for 20 to 25 minutes, until the centers are set and no longer runny.
Top some cups with the reserved bacon and cheddar.
Return the tin to the oven briefly, just until the cheese melts.
Remove from the oven, cool briefly, and serve.