Ultrafiltration (UF) is a low-pressure membrane that yields higher permeate flux and saves significant operating costs compared to high-pressure membranes; however, studies addressing the combined improvement of anti-organic and biofouling properties of UF membranes are lacking. This study investigated the fouling resistance and antimicrobial property of a UF membrane via silver phosphate nanoparticle (AgPNP) embedded polyelectrolyte (PE) functionalization. Negatively charged polyacrylic acid (PAA) and positively charged polyallylamine hydrochloride (PAH) were deposited on the membrane using a fluidic layer-by-layer assembly technique. AgPNPs were immobilized within the crosslinked “bilayers” (BL) of PAH/PAA. The effectiveness of AgPNP immobilization was confirmed by microprofile measurements on membrane surfaces using a solid contact Ag micro-ion-selective electrode. Upon stable and uniform BL formation on the membrane surface, the permeate flux was governed by a combined effect of PAH/PAA-derived hydrophilicity and surface/pore coverage by the BLs “tightening” of the membrane. When fouled by a model organic foulant (humic acid), the functionalized membrane exhibited a lower flux decline and a greater flux recovery due to the electrostatic repulsion imparted by PAA when compared to the unmodified membrane. The functionalization rendered antimicrobial property, as indicated by fewer attachments of bacteria that initiate the formation of biofilms leading to biofouling.