Heat 2 tablespoons olive oil in a large skillet over medium-low heat. Add the sliced onions, salt, and pepper. Cook, stirring occasionally, until deeply golden brown, 30-40 minutes.

In a separate large skillet, heat 1 tablespoon olive oil over medium-high heat. Add the sliced apples and cook, turning occasionally, until the apples are soft and beginning to brown, about 5 minutes.

Place the chopped bacon in a cold skillet. Turn the heat to medium and cook, stirring occasionally, until browned, about 8 minutes.

Preheat the oven to 425°F.

Brush the pizza crusts with olive oil. Sprinkle ¾ cup of cheese evenly on each crust. Divide the caramelized onions evenly between the crusts and place the apple slices in a circle, overlapping them slightly. Top with the cooked bacon and cook for 7 minutes or until the cheese is melted. Cut into slices and serve immediately.