In a large Dutch oven or saucepan, melt the 2 tablespoons of butter over medium-high heat. Add chopped onion and cook until softened, about 5 minutes.
Add 4 cups cubed squash and diced apple and sauté for 5 more minutes. Pour in 2 cups stock and ½ cup apple cider. Season it with ¼ teaspoon nutmeg, ¼ thyme, ½ teaspoon salt, and ½ teaspoon pepper. Bring to simmer, cover and cook until squash is tender, about 20 minutes.
Using an immersion blender, puree until smooth or desired consistency. Alternatively, remove squash chunks with a slotted spoon and puree in a blender or food processor, then return the squash to the pot and stir until combined.
Serve immediately or refrigerate for up to three days.
If the soup is too thick, you can dilute it by adding water or broth.
For the best results, read additional tips in the post above.
Please keep in mind that nutritional information is a rough estimate and can vary significantly based on products used.