Preheat oven to 350°F (175°C). Spray a 12-cup muffin tin with nonstick cooking spray or use silicone liners.
In a large bowl, whisk together eggs and cottage cheese until well combined and slightly fluffy.
Add remaining ingredients (cheese, veggies, seasonings, and any optional proteins). Stir until evenly mixed.
Pour mixture evenly into the muffin cups, filling each about ¾ full.
Bake for 22–25 minutes, or until the tops are golden and set. A toothpick inserted should come out clean.
Cool slightly, then remove from the muffin tin. Store in the fridge for up to 5 days or freeze for up to 2 months.