Membrane bioreactors (MBRs) effectively remove particulate and microbial contaminants, yet the role of membrane fouling in regulating phage-associated antibiotic resistance genes (pARGs) remains unclear. Here, a laboratory-scale MBR treating real domestic wastewater was operated across three fouling phases to track pARG redistribution and evaluate membrane cleaning. Although effluent pARG relative abundance was, on average, 94.9% lower than influent levels, severe fouling was associated with increased effluent pARG abundance, subtype richness, and risk. Effluent pARG subtypes increased from 7 to 23, with trimethoprim-associated pARGs accounting for 73.91% during late fouling, while effluent profiles became increasingly similar to membrane-biofilm profiles. Predicted lytic phages remained dominant, and distinct pARG–virus–host associations were identified, with dfrC emerging as a potential key node. EPS remodeling, elevated reactive oxygen species, and enhanced antioxidant responses were consistent with early- to middle-stage pARG retention and increased effluent occurrence under severe fouling. Under the tested conditions, citric acid cleaning showed an apparent trend toward more extensive composite-fouling removal and a more sustained low-pARG trajectory than ultrapure-water backwashing. These findings identify membrane biofilms as important interfaces associated with pARG retention and redistribution and highlight pARG occurrence as a consideration in membrane-cleaning strategies.