Preheat the oven to 325°F (165°C).
Lightly grease a 12-cup muffin tin or use silicone liners.
Add eggs, cottage cheese, milk, salt, pepper, garlic powder, and onion powder to a blender. Blend until completely smooth, about 20–30 seconds.
Stir in the shredded cheese and your chopped add-ins. If using watery veggies like tomatoes or mushrooms, pat them dry first.
Divide the mixture evenly among the muffin cups, filling each about 3/4 full.
For extra tenderness, place the muffin tin on a sheet pan and pour hot water into the pan to create a shallow water bath. This is optional but helps prevent rubbery edges.
Bake for 18–22 minutes, or until the centers are just set and no longer jiggly.
Do not overbake.
Cool in the pan for 5 minutes, then run a knife around the edges and lift out. Serve warm or let cool completely for meal prep.