Coat a large nonstick pan with cooking spray. Warm pan over medium heat. Add onions and reduce heat to medium low. Cook for 15 to 20 minutes, stirring frequently, until onion browns and become very fragrant.
Meanwhile, prepare pizza crust for baking according to package directions. Mince tomatoes and crumble cheese. Tear spinach into pieces. Preheat oven to 425.
Spread caramelized onions on pizza crust and bake for 12 minutes. Remove from oven and add tomatoes, spinach, and cheese. Bake until cheese is melted, about 3 more minutes. Season with pepper and serve.