Preheat the oven: Set to 350°F (175°C). Lightly grease a 12-cup muffin tin with oil or cooking spray. Silicone liners also work great.
Cook the sausage: In a skillet over medium heat, crumble and cook the sausage until browned and cooked through, about 6–8 minutes.
Drain excess fat if needed. Let it cool slightly.
Sauté the veggies (optional but recommended): In the same pan, add a drizzle of oil if needed. Cook the onion and bell pepper for 3–4 minutes until softened.
Stir in the spinach for 30–60 seconds until wilted. Remove from heat and cool briefly.
Whisk the eggs: In a large bowl, whisk the eggs with milk, salt, pepper, and any optional seasonings until well combined.
Add mix-ins: Stir in the cooked sausage, sautéed veggies, and most of the cheese, reserving a small handful for topping.
Fill the muffin tin: Divide the mixture evenly among the 12 cups, filling about 3/4 full. Sprinkle the remaining cheese on top.
Bake: Place in the oven for 18–22 minutes, until the muffins are set and slightly puffed.
A toothpick should come out mostly clean.
Cool and release: Let the muffins sit in the tin for 5 minutes, then run a thin knife around the edges to lift them out. Transfer to a rack to cool.
Serve: Enjoy warm, or let them cool fully for storage.