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In medium-size soup pot over medium heat, add ghee and sliced onions. Stir onions to coat, then sprinkle with salt. Cook for 20-25 minutes or until onions begin to brown.
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Stir in garlic and turn heat down slightly. Continue cooking and stirring occasionally until onions start sticking to the bottom of pan (careful not to burn).
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Add tomato paste, stir and cook for 5 minutes until browned.
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Add wine and stir to remove cooked bits at bottom of pan.
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Add thyme, bay leaves, mushroom stock, vegetable stock, Worcestershire sauce and ground pepper. Stir to combine.
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Bring soup to a boil, cover pan, turn down heat to simmer and cook for 15 minutes.
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Preheat oven to broil. Ladle soup into oven-safe bowls and garnish with croutons and shredded vegan mozzarella. Place dishes on sheet pan and transfer to oven. Broil for several minutes or until cheese is melty and lightly browned.