Place the cubed butternut squash, chopped apples, and diced onion into the slow cooker.
Pour the vegetable broth over the vegetables and fruit.
Add the cinnamon, nutmeg, salt, and black pepper. Stir gently to combine.
Cover and cook on low for 6 hours or until the squash is very soft.
Use an immersion blender to puree the soup directly in the slow cooker until smooth. If using a countertop blender, work in batches and return the soup to the slow cooker.
Toast the pumpkin seeds in a dry skillet over medium heat for 3 to 4 minutes, stirring often, until lightly golden.
Ladle the soup into bowls and sprinkle the toasted pumpkin seeds on top before serving.