Prep the oven and pan: Heat oven to 350°F (175°C).
Spray a 12-cup muffin tin well or use silicone liners to prevent sticking.
Cook the veggies (if needed): If using watery vegetables like mushrooms, zucchini, or spinach, sauté them in a little oil over medium heat for 3 to 4 minutes to soften and release moisture. Let cool slightly.
Whisk the base: In a large bowl, whisk eggs, cottage cheese, salt, pepper, garlic powder, and red pepper flakes until smooth. For extra-smooth texture, blend the eggs and cottage cheese in a blender for 10 to 15 seconds.
Add mix-ins: Stir in shredded cheese, chopped herbs, cooled vegetables, and any cooked meats.
Mix gently to distribute evenly.
Fill the cups: Divide the mixture among the muffin cups, filling each about 3/4 full. Stir the bowl between pours so the solids don’t settle.
Bake: Bake 18 to 22 minutes, until the centers are set and a toothpick comes out clean. The muffins will puff up and then settle slightly as they cool.
Rest and release: Cool in the pan for 5 minutes, then run a thin knife around the edges to loosen.
Transfer to a rack to finish cooling.
Serve: Enjoy warm, or cool completely for storage. A sprinkle of extra herbs or hot sauce on top is great.