Prep the pan: Heat oven to 350°F (175°C).
Grease a 12-cup muffin tin with cooking spray or a thin layer of oil.
Cook the veggies: If using raw onions, peppers, or mushrooms, sauté in a little oil with a pinch of salt until softened and excess moisture cooks off. Let cool slightly.
Whisk the base: In a large bowl, whisk eggs, cottage cheese, and milk (if using) until mostly smooth. It won’t be perfectly blended—that’s fine.
Stir in salt, pepper, and shredded cheese.
Fold in add-ins: Stir in the cooled veggies, cooked protein, and herbs. Taste a small spoonful and adjust seasoning if needed.
Fill the cups: Divide the mixture evenly among the muffin cups, filling about 3/4 full. Give the pan a gentle tap to level.
Bake: Place on the middle rack and bake 16–20 minutes, until the centers are just set and the tops look slightly puffed.
A toothpick should come out mostly clean.
Rest and release: Cool in the pan for 5 minutes, then run a thin knife around edges to loosen. Transfer to a rack to finish cooling.
Serve or store: Enjoy warm, or pack for later. Add hot sauce, salsa, or a dollop of Greek yogurt if you like.