Place mozzarella in freezer for approximately 15 minutes in order to get it hard enough to hand grate or shred using a food processor.
Preheat oven to 450 degrees. Line a rimmed baking sheet with foil and spray with non-stick cooking spray. Place mushroom caps, gill-side up, on the baking sheet. Sprinkle with 1/8 teaspoon pepper. Roast until tender, about 20-25 minutes.
Meanwhile, blend ricotta cheese, spinach, Parmesan cheese, mozzarella cheese, Italian seasoning, half of the minced garlic and half of the minced onion in a medium bowl. Season with salt and pepper. Place the marinara sauce in a small pot with the remaining minced garlic and onions. Heat on low until heated through.
When the mushroom caps are tender, carefully pour out any liquid in the caps. Return the caps to the baking sheet, gill-side up. Spread 1 to 2 tablespoons of marinara sauce into each mushroom cap; cover the remaining sauce and keep warm. Mound a generous 1/3 ricotta/spinach filling into each mushroom cap. Bake until hot, about 10 minutes. Serve with remaining sauce.