A key step in macroautophagy is the formation of autolysosomes through the fusion of autophagosomes with lysosomes. After fusion, lysosomal enzymes degrade both the inner autophagosomal membrane and its enclosed contents. However, the detailed mechanisms underlying inner membrane degradation remain unclear. We previously demonstrated that conjugation of ATG8 to phosphatidylethanolamine (PE) plays a crucial role in the degradation of the autophagosomal inner membrane (Tsuboyama et al., 2016, Science). In this study, we observed abnormal localization of the autophagosome–lysosome tethering factors PLEKHM1 and EPG5 in ATG8–PE-deficient cells. In wild-type cells, mature autophagosomes acquire STX17, which enables their fusion with lysosomes. PLEKHM1 is recruited to these STX17-positive autophagosomes, while EPG5 is recruited only to a limited extent. In contrast, ATG8–PE-deficient cells fail to recruit PLEKHM1 but show an unexpected increase in EPG5 recruitment. In wild-type cells, STX17-positive autophagosomes displaying a LysoTracker ring pattern—indicating acidification only in the intermembrane space—persist for about 10 minutes before the inner membrane is degraded, resulting in full LysoTracker positivity. In cells lacking both PLEKHM1 and EPG5, this LysoTracker ring pattern persists for over 30 minutes, similar to what is observed in ATG8–PE-deficient cells. Importantly, this prolonged phenotype requires the ATG8-binding domains of both PLEKHM1 and EPG5. These results suggest that proper ATG8–PE-dependent recruitment of PLEKHM1 and EPG5 is important for the timely and efficient degradation of the autophagosomal inner membrane after fusion.