Preheat oven to 350 °F. Lightly coat a 9×13-inch baking dish with cooking spray. In a small bowl, combine cup mozzarella cheese and 1 Tbsp. Parmesan cheese. Set aside.
In a medium bowl, mix remaining mozzarella and Parmesan cheeses with cottage cheese. Set aside.
Preheat the oven to 400˚F. Line a large baking sheet with aluminum foil. Lightly coat the foil with cooking spray.
Put the beets on the baking sheet. Drizzle with 1 Tbsp. oil. Roast for 45 to 55 minutes, or until the beets are tender when pierced with a fork.