Preheat the oven to 350°F (175°C). Generously grease a 12-cup standard muffin tin or use silicone muffin liners.
Place the eggs, cottage cheese, salt, pepper, garlic powder, and onion powder into a high-speed blender.
Process on high for 30 to 45 seconds until the mixture is completely smooth and contains no cottage cheese curds.
Distribute the chopped spinach evenly into the bottom of the 12 muffin cups.
Stir the shredded cheddar and Parmesan cheese into the egg mixture by hand.
Pour the mixture into the muffin cups, filling each approximately three-quarters full.
Bake for 22 to 25 minutes until the egg bites are set and the centers no longer jiggle when the pan is moved.
Remove from the oven and let rest for 5 to 10 minutes in the pan; the bites will deflate slightly as they cool.
Carefully run a thin spatula or knife around the edges to release from the tin and serve.