Prep the pan: Heat the oven to 350°F (175°C). Grease a 12-cup muffin pan well with oil or nonstick spray.
For easy release, you can also use silicone liners.
Whisk the base: In a large bowl, whisk the eggs until smooth. Add cottage cheese and whisk again until mostly combined. A few curds are fine.
Season: Stir in salt, pepper, garlic powder, and any optional spices.
Fold in shredded cheese.
Add mix-ins: Gently fold in chopped veggies, herbs, and cooked protein if using. Tip: If your veggies are very watery (like spinach or mushrooms), sauté them first and pat dry.
Fill the cups: Divide the mixture evenly among the muffin cups, filling each about 3/4 full.
Bake: Place the pan on the middle rack and bake for 18–22 minutes, until the centers are set and the tops look slightly puffed and lightly golden.
Cool: Let the egg cups rest in the pan for 5 minutes. Run a thin knife around the edges, then lift them out. Cooling helps them firm up.
Serve: Enjoy warm, or let them cool completely for storage.