A system and method automatically generates a root volume for use by a storage operating system of a storage system. During initialization of the storage system, the storage operating system detects that no operational root volume exists and, in response, invokes a root volume generation process. The root volume generation process automatically creates a thinly provisioned flexible volume of the smallest allowable size on an aggregate. The created flexible volume is marked as the root volume for the storage system. The storage operating system then continues initialization utilizing the automatically generated root volume.