Add the butter to a large pot over medium heat. Add the onions and sauté for about 20-30 minutes, stirring frequently, until caramelized.
Add the garlic and cook for another minute. Pour in the wine and let it simmer for 2 minutes.
Stir in the beef stock, bay leaf, and thyme. Simmer for about 10-15 minutes.
While soup is cooking, make your chaffles. Mix together the mozzarella, cheddar, and egg. Spoon out enough batter to just fill a mini waffle maker. Cook until done. Repeat with the remaining batter (this should make about 6 small chaffles).
Discard the bay leaf and thyme, then ladle your soup into oven safe dishes. Place a chaffle on top of the soup and then add some shredded Gruyere cheese on top of that. Broil for 2-3 minutes until cheese is melted. Enjoy!