Purpose <p>Children with inner ear malformations, particularlyIncomplete Partition Type II (IP-II), often exhibit variability in auditory and cognitive outcomes despite receiving appropriate rehabilitation. This study aimed to compare phoneme discrimination, executive functions, verbal memory, and hearing-related quality of life in children with IP-II using cochlear implants against peers with normal cochlear anatomy (using hearing aids or implants) and normal hearing.</p> Methods <p>Fifty-eight children (aged 7–10 years) were divided into four groups: hearing aid users (HA), cochlear implant users with normal anatomy (CI), CI users with IP-II(CI), and normal-hearing controls. The test battery included the Auditory Speech Sound Evaluation (ASSE), Stroop Test, Working Memory Scale, and HEAR-QL-26. Regression analyses examined predictors of cognitive outcomes.</p> Results <p>Phoneme discrimination accuracy differed significantly among groups (<i>p</i> &lt; 0.001), with the IP-II(CI) group demonstrating the lowest performance. Verbal memory levels also differed significantly (<i>p</i> = 0.014), with the HA group showing a notably higher proportion of “very low” performance. While no significant differences were found in Stroop performance, descriptively longer completion times were observed in hearing-impaired groups. Quality of life scores were significantly lower in all hearing-impaired groups (<i>p</i> &lt; 0.01). Regression analyses indicated that duration of device use was a significant predictor of interference control (Stroop Level 5: β=−0.45,<i>p</i> = 0.002).</p> Conclusion <p>Children with IP-II exhibit reduced phoneme discrimination and verbal memory vulnerabilities despite comparable aided thresholds. These findings highlight the necessity of incorporating phoneme-level and cognitive assessments into routine follow-up, as audiological measures alone may underestimate functional listening challenges.</p>