Background: To perform a multimodal assessment of the ectopic inner foveal layers’ (EIFL) prognostic role on idiopathic epiretinal membrane (ERM) surgery. Methods: We retrospectively followed-up for 12 months 27 patients who underwent ERM surgery and stratified them based on EIFL presence (group 1) or absence (group 2) at baseline. Central Retinal Thickness (CRT) and best-corrected visual acuity (BCVA) were compared pre- and post-operatively at 1, 4 and 12 months, whereas fixation stability (FS), macular sensitivity (MS) and multifocal electroretinogram (mfERG) responses were confronted at baseline and 12 months. Results: In group 1, BCVA improved at 4 and 12 months (MD = 0.14 (SE = 0.04); MD = 0.13 (SE = 0.05), respectively) as well as in group 2 (MD = 0.31 (SE = 0.07); MD = 0.41 (SE = 0.08), respectively). CRT did not change in group 1, whereas it decreased in group 2 at 4 and 12 months (MD = −73.13; SE = 23.56; MD = −76.20; SE = 23.56). MS showed no changes in both groups after surgery. FS did not change in group 1, whereas group 2 improved FS 2° (+8.91 ± 13.97) and FS 4° (+4.33 ± 3.84). MfERG P1 wave did not change in group 1, while in group 2 αP1-2, αP1-3 and αP1-4 improved postoperatively (27.97 ± 27.62; 12.51 ± 17.36; 10.49 ± 17.19, respectively). Conclusions: Multimodal assessment confirmed that EIFL negatively affected ERM surgery outcomes.