Prep the pan: Heat the oven to 350°F (175°C). Grease a standard 12-cup muffin tin well or line with silicone liners.
Blend the base: In a large bowl, whisk eggs, cottage cheese, salt, pepper, and spices until smooth.
For an ultra-smooth texture, blend with an immersion blender.
Add mix-ins: Stir in shredded cheese, vegetables, cooked protein, and herbs. Keep the mix-ins small and evenly chopped.
Fill the cups: Divide the mixture among the 12 cups, filling about 3/4 full. Give the tin a gentle tap to level.
Bake: Bake for 18–22 minutes, until the centers are just set and the tops are lightly golden.
Cool: Let muffins cool in the pan for 5 minutes, then loosen edges with a knife and transfer to a rack.
Serve or store: Enjoy warm, or cool completely before storing.