Integrating biocidal nanoparticles (NPs) into polyamide (PA) membranes shows promise for enhancing resistance to biofouling. Incorporating techniques can tailor thin-film nanocomposite (TFN) membranes for specific water purification applications. In this study, silver-based metal-organic framework Ag-MOFs (using silver nitrate and 1,3,5-benzentricarboxylic acid as precursors) are incorporated into PA membranes via three different methods: i) incorporation, ii) dip-coating, and iii) in situ ultrasonic techniques. The characterizations, such as top-surface and cross-section scanning and transmission microscopy, reveal that the incorporation methods for the modified TFN membranes substantially control morphology and surface characteristics. For example, the in situ ultrasonically interlayered Ag-MOFs showed the largest pores (average pore diameter of 14 Å ± 0.1), resulting in the highest water permeance (water flux of 10.9 LMH/bar for NaSO). It also show superior antifouling and anti-biofouling performance, with a flux recovery ratio (FRR) of 94.1% in both fouling tests due to its improved surface hydrophilicity and the antibacterial properties of incorporated Ag-MOFs. Conversely, the surface-grafted dip-coated Ag-MOFs offered the highest salt rejection, attributed to its highly negatively charged surface and a dense PA network with narrow pores (average pore diameter of 10 Å ± 0.06).