Heat olive oil in a skillet over medium-high heat. Cook and stir onion with salt in the hot oil until onion is lightly browned, 10 to 15 minutes. Stir crushed red pepper, black pepper, and garlic into onion; cook until garlic is fragrant, about 1 minute.
Stir black beans and tomatoes into onion mixture and cook until mixture is heated through, about 5 minutes. Remove from heat. Add spinach and cover to allow spinach to wilt, about 3 minutes. Toss and serve.