Heat the oil in the pressure cooker. Cook the shallots for 3 minutes until soft with frequent stirring. Turn off the pressure cooker.
Stir in the squash, broth, ginger root, salt, and pepper. Cook on high pressure for 20 minutes. Allow the pressure to release naturally for 10 minutes, then quickly release any remaining pressure. Turn off the pressure cooker. Remove the pressure cooker lid.
Allow the soup to cool slightly. Working in batches, transfer the soup to a blender and puree until smooth. Return the soup to the pressure cooker.
Cook for 2 to 3 minutes, or until heated through, stirring frequently. Ladle the soup into bowls. Sprinkle with the nutmeg.