Preheat oven to 400 degrees. Lightly oil a baking sheet or coat with nonstick spray.
Place butternut squash, onion, bell pepper and bacon in a single layer onto the prepared baking sheet. Add olive oil and garlic; season with salt and pepper to taste. Gently toss to combine.
Bake in preheated oven for 25-30 minutes, or until butternut squash is tender, stirring at halfway point.
Heat a large skillet over medium high heat. Add bacon and cook until brown and crispy, about 6-8 minutes. Transfer to a paper towel-lined plate.
Heat a large stockpot or Dutch oven over medium heat. Add butternut squash mixture and thyme, stirring occasionally until fragrant, about 1-2 minutes. Season with salt and pepper to taste. Using an immersion blender, stir in chicken stock and puree.
Bring to a boil, reduce heat and simmer until slightly thickened, about 5-10 minutes. If the soup is too thick, add more chicken stock as needed until desired consistency.
Serve immediately. If desired, garnish with bacon, goat cheese and chives.
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