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Add the celery, carrots, onion, stock, water, salt, thyme, bay leaf, and chicken to a large stock pot or Dutch oven. Bring to a boil over medium heat. Cover with lid, reduce heat to medium/low, and let simmer for 45 minutes.
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Remove chicken. Using two forks, shred the chicken breasts, and then add back to the pot.
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Add the quinoa. Keep the soup at a simmer over medium/low heat. Simmer the soup for about 20 minutes, until the quinoa is cooked.
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In a separate small mixing bowl, whisk together the milk and flour. Pour the slurry into the soup. Increase the heat to medium, keep mixing the soup, and cook until the soup thickens. About 10-15 minutes.
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Shut the heat off, add the lemon juice and freshly ground black pepper. Add the juice from 1 1/2 lemons, taste and then see if you want more lemon or not. Remove the bay leaf and then serve.