Cut the butternut squash in half and scoop out the seeds. Place both halves, cut side down in a microwave-safe dish and add a quarter inch of water to the dish. Cover with plastic wrap and cook in the microwave for 10-15 minutes or until it can be easily pierced with a fork. Scoop out the squash and set aside.
Fry onions and garlic in butter in a large pot. Stir in chicken broth, apple juice, butternut squash puree and pumpkin puree. Bring to a boil over medium heat, stirring occasionally. Turn the heat to low and simmer for 10 minutes, stirring often. Stir in nutmeg, pepper, and salt.
Use an immersion blender to blend until smooth. Or carefully pour the soup into a vented, high-speed blender (leave the center cap off the lid and cover with a dish towel) and blend until smooth. This step can be done in batches if necessary.