Cross-modal reorganization in the auditory cortex has been reported in deaf individuals. However, it is not well understood whether this compensatory reorganization induced by auditory deprivation recedes once the sensation of hearing is partially restored through a cochlear implant. The current study used electroencephalography source localization to examine cross-modal reorganization in the auditory cortex of post-lingually deafened cochlear implant users. We analysed visual-evoked potentials to parametrically modulated reversing chequerboard images between cochlear implant users (n = 11) and normal-hearing listeners (n = 11). The results revealed smaller P100 amplitudes and reduced visual cortex activation in cochlear implant users compared with normal-hearing listeners. At the P100 latency, cochlear implant users also showed activation in the right auditory cortex, which was inversely related to speech recognition ability with the cochlear implant. These results confirm a visual take-over in the auditory cortex of cochlear implant users. Incomplete reversal of this deafness-induced cortical reorganization might limit clinical benefit from a cochlear implant and help explain the high inter-subject variability in auditory speech comprehension.