Objectives Cochlear implant infections may be refractory to medical management and require device removal with subsequent reimplantation. During device removal, the intracochlear electrode array is commonly left in place to prevent obliteration of the cochlear lumen. If the electrode is colonized with pathogens, this risks contaminating the replacement implant. In this study, we compare the microorganisms detected on infected cochlear implants against those on the retained electrode using culture and microbial gene-sequencing techniques. Study Design Prospective single-cohort study. Setting Tertiary medical center. Subjects and Methods Six patients with refractory cochlear implant infections had the receiver-stimulator and extracochlear electrode removed to facilitate treatment of the infection. The intracochlear electrode was removed at (delayed) reimplantation. Implant specimens were analyzed by microbial culture and 16S DNA gene sequencing. Results Staphylococcus aureus was the organism most commonly identified. None of the 6 patients' intracochlear electrodes yielded microbes by culture. Two intracochlear electrodes revealed bacterial species, and 1 revealed fungal species by gene sequencing. There was no correlation between the microbes on the infected extracochlear implants and the retained intracochlear electrodes. All subjects underwent reimplantation after resolution of their infections. One of 6 subjects developed a second infection after reimplantation, with S aureus in the primary and secondary infections. Conclusions The intracochlear electrodes of infected cochlear implants carry a low microbial burden. Preserving intracochlear electrodes upon removal of infected cochlear implants appears to carry a low risk of contaminating a replacement cochlear implant.