A method is described for surgical implantation of a cochlear implant system. An intraoperative baseline value stapedial reflex response is determined for a cochlear implant patient. Then while performing a given step in a multi-step surgical process to implant a cochlear implant system in the patient, the stapedial reflex response is monitored, and if the stapedial reflex response changes from the baseline value response more than a safe change threshold value, the given step is stopped.