<b><i>Purpose:</i></b> This study aimed to investigate the long-term effect of observed epiretinal membranes on the outer retinal layers and visual acuity. <b><i>Methods:</i></b> It is a retrospective observational study. Subjects with an epiretinal membrane and consecutive optical coherence tomography scans were followed for changes in visual acuity, central macular thickness, ellipsoid zone loss, and outer foveal thickness (OFT). <b><i>Results:</i></b> The study consisted of 24 eyes of 22 patients, with a mean follow-up of 5 ± 1.6 years. The mean visual acuity was slightly worse at the last follow-up (0.22 ± 0.36 LogMAR [20/33] vs. 0.27 ± 0.36 LogMAR [20/36], <i>p</i> = 0.05). Ellipsoid zone loss was found in 37.5% of eyes. Vision loss was associated with initial size of ellipsoid disruption (<i>p</i> = 0.048) and age (<i>p</i> = 0.027). A decrease in OFT was associated with an initially larger zone of ellipsoid disruption (<i>p</i> = 0.006) and an initially thicker OFT (<i>p</i> = 0.011). An epiretinal membrane associated with vitreomacular adhesion within 1,000 μm of the foveal center at baseline was associated with ellipsoid zone loss (<i>p</i> = 0.012) but not with a change in visual acuity. <b><i>Conclusions:</i></b> Ellipsoid zone changes were common in this study and tended to enlarge over time. Epiretinal membranes associated with vitreomacular adhesion within 1,000 μm of the foveal center may be a risk factor for ellipsoid zone loss.