In a large pot, heat the oil over medium heat. Add the onion and cook, stirring occasionally until they start to brown, around 5-8 minutes. Reduce the heat to medium-low.
Stir in the garlic cloves, and cook for 1-2 minutes. Stir in the cinnamon, clove, and nutmeg, stirring constantly for 1 minute until very fragrant. Add the squash, apple, salt, and pepper. Stir in 3 cups vegetable broth, scraping the bottom of the pot with the spoon to release any browned bits.
Bring to a simmer and cook, stirring occasionally, until the squash and apple are very tender, 30 to 40 minutes. Remove from the heat.
Carefully transfer the soup to a blender with the center part of the top removed. Puree the soup until smooth. *see note
Add additional broth for a thinner consistency. Taste and adjust seasoning as desired.
Add the butter, lemon juice, and blend for a few more seconds. Serve topped with optional chopped thyme, and enjoy!