In a deep skillet, heat 2 tablespoons extra-virgin olive oil over medium heat. Add the onions and cook, stirring occasionally, until translucent and softened, about 15 minutes. Add the wine and bring to a boil. Pour in the beef broth, lower the heat to low and simmer for 10 minutes; season with pepper.
Preheat the broiler. Divide the soup among 4 ovenproof bowls, then top each with one-quarter of the croutons and a slice of cheese. Set the bowls on a rimmed baking sheet and broil until the cheese is bubbly and golden, about 1 minute.