Cook bacon in large pot over medium-high heat until crisp. Using slotted spoon, transfer bacon to paper towels to drain.
Pour off all but cup drippings from pot. Add butter to pot; melt over medium-high heat. Add onions and 1 cup bell pepper. Saute until onions are soft, about 10 minutes. Add flour; stir 2 minutes. Mix in broth, then squash, potatoes, and thyme; bring to boil. Reduce heat to medium-low; simmer uncovered until squash and potatoes are tender about 10 minutes. (Can be made 1 day ahead. Cool. Chill uncovered until cold, then cover and keep chilled. Bring to simmer before continuing.) Add chicken (purchased roast chicken), 1 cup green onions, and cup cilantro; simmer 5 minutes. Season with salt and pepper.
Ladle chowder into bowls; sprinkle with remaining 1 cup green onions and 2 tablespoons cilantro.
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