Objective. Subretinal prostheses electrically stimulate the residual inner retinal neurons to partially restore vision. We investigated the changes in neurosensory macular structures and it is thickness associated with subretinal implantation in geographic atrophy (GA) secondary to age-related macular degeneration (AMD). Approach. Using optical coherence tomography, changes in distance between electrodes and retinal inner nuclear layer (INL) as well as alterations in thickness of retinal layers were measured over time above and near the subretinal chip implanted within the atrophic area. Retinal thickness (RT) was quantified across the implant surface and edges as well as outside the implant zone to compare with the natural macular changes following subretinal surgery, and the natural course of dry AMD. Main results. GA was defined based on complete retinal pigment epithelium and outer retinal atrophy (cRORA). Based on the analysis of three patients with subretinal implantation, we found that the distance between the implant and the target cells was stable over the long-term follow-up. Total RT above the implant decreased on average, by 39 ± 12 µm during 3 months post-implantation, but no significant changes were observed after that, up to 36 months of the follow-up. RT also changed near the temporal entry point areas outside the implantation zone following the surgical trauma of retinal detachment. There was no change in the macula cRORA nasal to the implanted zone, where there was no surgical trauma or manipulation. Significance. The surgical delivery of the photovoltaic subretinal implant causes minor RT changes that settle after 3 months, and then remain stable over long-term with no adverse structural or functional effects. Distance between the implant and the INL remains stable up to 36 months of the follow-up.