Preheat oven to 350 degrees F and grease 2 (9x13 inch) baking dishes with cooking spray. Set aside.
Place cottage cheese, 1/2 of the mozzarella, 1/2 cup of the parmesan, Italian seasoning, basil, garlic powder, onion powder, nutmeg, salt, pepper, and eggs into a food processor.
Process until combined. It’s okay if it's still a little chunky.
Pulse in spinach until it’s incorporated. Set aside.
Pour half the sauce into the bottom of the prepared pans.
Place cottage cheese mixture into a gallon sized ziplock baggie, seal, then snip one corner of the baggie with scissors.
Pipe filling into each manicotti shell and arrange over sauce.
Pour remaining sauce over top, then sprinkle with remaining mozzarella, and 1/4 cup Parmesan cheese.
Bake in preheated oven for 30 minutes, or until hot and bubbly.