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Heat olive oil in a large Dutch oven or soup pot over medium heat. Add onion and sprinkle with salt and pepper. Cook, stirring occasionally, until softened and translucent, about 5 minutes.
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Add garlic, ginger, cumin, and cinnamon. Stir and cook for 1 minute.
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Add butternut squash, broth, thyme, salt, and pepper. Make sure there is enough broth to cover the squash. Add more broth or water if needed. Stir to combine.
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Bring to a boil then reduce heat to a simmer. Cover and simmer until squash is tender, about 30 minutes.
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Remove and discard thyme stems (the leaves should fall off during the cooking process).
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Place 1/4 of both beans in a small bowl and mash with a fork. Add both beans and mashed beans to the pot and stir to combine.
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Cook until beans are heated through, about 5 minutes.
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Ladle soup into bowls and top with a heaping tablespoon or two of couscous mixture.