Heat oil in a large pot over medium heat; sauté onion until translucent, 4–5 minutes. Add garlic and cook 30 seconds.
Add squash and apples; stir to coat, then pour in broth and apple juice. Bring to a simmer, cover, and cook 15–20 minutes until squash is tender.
Use an immersion blender or transfer in batches to a blender; puree until smooth. Return to pot and stir in yogurt or cream if using.
Season with nutmeg, cinnamon (if using), salt, and pepper. Warm gently for 2–3 minutes and adjust seasoning.
Serve topped with chives or pepitas.