Cochlear implants (CI) candidates with chronic otitis media require special attention and management. The need of opening of the inner ear creates potential routes of spread of infection to subarachnoid spaces and lead to meningitis. The aim of the study was to analyse the technique and complications of subtotal petrosectomy (SP) in cochlear implant candidates with chronic otitis media at three different CI centres. A retrospective study was carried out in three Territory Referral Hospitals. The centres follow Fisch’s philosophy and surgical techniques of SP. The study group consisted of 19 patients, 4 men and 15 women, aged 12–82 years. All patients underwent SP with either primary or staged CI implantation. Indications for single or a staged management, difficulties during surgery and complications were analysed. Skin and muscle flap design in primary and revision cases as well as imaging follow-up strategy are discussed. In 14 patients implantation was performed in a single stage and in 5 cases in two stages. Follow-up ranged from 8 months to 10 years. All the patients use their implants and there were no major nor minor complications. The use of subtotal petrosectomy with cochlear implants is a safe and efficient technique when strict surgical steps and rules are applied. Closure of the external ear canal after previous meatoplasty can be challenging and extreme care dissecting the skin flaps is required. In patients with extensive cholesteatoma, active discharge from the ear with resistant bacteria or an “unstable” situation, the procedure can be staged.Electronic supplementary materialThe online version of this article (doi:10.1007/s00405-015-3573-1) contains supplementary material, which is available to authorized users.