Preheat oven to 375°F. Lightly oil a 9x13-inch baking dish.
Slice tomato tops, scoop out centers, and sprinkle insides with a pinch of salt. Invert to drain 10 minutes.
Warm olive oil in a large skillet over medium heat. Soften onion and bell pepper, 4 to 5 minutes.
Stir in garlic for 30 seconds. Add ground beef and cook, crumbling, until browned. Drain excess fat.
Mix in taco seasoning, tomato paste, and water. Simmer 2 minutes until glossy and thickened.
Fold in black beans, corn, and cooked rice. Stir in lime juice and cilantro. Season with salt and pepper.
Nest tomatoes in the dish. Pack with filling and mound cheese on top of each.
Bake 15 to 18 minutes until tomatoes are just tender and cheese is bubbling. Rest 5 minutes.
Serve warm with sour cream and green onions.