Inner ear malformations and cochlear implant positioning are often associated with challenging surgical procedures, considering the highly variable anatomy of the temporal bone in malformed ears. Preoperative classification (e.g., Sennaroglu system) and intraoperative adaptability are key to safe and effective hearing restoration in these patients. An adequate preoperative imaging study through CT scan and MRI is of utmost importance, as a deep counseling regarding results expectation. Critical concerns include cerebrospinal fluid (CSF) leak due to modiolar defects, cochlear nerve anomalies, and atypical facial nerve courses. Subtotal petrosectomy (SP) is the preferred approach in high-risk cases, offering surgical control and multi-layer protection against CSF leakage. From a surgical point of view, middle ear malformations (often associated with the inner ear ones) may represent even a greater challenge for the surgeon, due to the absence of the standard anatomical landmarks.