Biofouling is a critical defect of the reverse osmosis (RO) system. It has been reported that disinfection processes tend to select certain undesirable disinfection-residual bacteria (DRB), leading to severe long-term biofouling potential. To provide constructive guidance on biofouling prevention in RO systems, this study evaluated the biofouling characteristics of RO membranes of DRB after the application of five mature disinfection methods (NaClO, NH2Cl, ClO2, UV, and O3) and two novel disinfection methods (K2FeO4 and flow-through electrode system (FES)). After a 32-day biofilm cultivation on the RO membranes, the DRB biofilm of K2FeO4 and O3 caused a slight normalised flux drop (22.4 ± 2.4% and 23.9 ± 1.7%, respectively) of RO membrane compared with the control group (non-disinfected, ~ 27% normalised flux drop). Moreover, the biofouling degree of the NH2Cl-DRB biofilm was similar to that of the control group. The remaining disinfection types aggravated membrane biofouling. The biofouling behaviour of DRB showed no relationship with bacterial concentration or activity. The thickness and density of the biofilms as well as the organics/bacterial number ratio in the DRB biofilm, helped explain the difference in the fouling degree between each group. Moreover, microbial community analysis showed that the relative abundance of typical highly secretory and biofouling-related genera, such as Pseudomonas, Sphingomonas, Acinetobacter, Methylobacterium, Sphingobium, and Ralstonia, were the main reasons for the difference in biofouling degree. All types of disinfection effectively prevented pathogen reproduction in the DRB biofilm. However, the relative abundance of (opportunistic) pathogens increased significantly after NaClO and ClO2 disinfection.