Previously, fouling of MD membranes was perceived to be minimal due to the operational conditions preventing bacterial growth. However, recent studies presented fouling of MD membranes, largely due to various halophilic and thermophilic bacterial. The current study presented potential of antibacterial cellulose nanocrystals (CNCs) capped silver nanoparticles (AgNPs) towards biofouling control in MD water desalination processes. Interestingly, the CNCs were used as capping and reducing agent in a microwave mediated synthesis of AgNPs. The green synthesis approach of AgNPs and its successful use in MD processes was reported for the first. The MD experiments were carried out using a series of modified PVDF membranes and feed solution spiked with a thermophilic G. stearothermophilus. Upon evaluation of fouled membranes, particularly PVDF, PVP-equipped PVDF, and f-CNTs-modified PVDF, the surface energy of interactions were −131 mJ/m2, −31.5 mJ/m2, −28.6 mJ/m2, suggesting favorable interaction between the membranes and bacterial foulant. The findings of this study were supported by fouling layer and bacterial growth as seen from scanning electron microscopy, atomic force microscopy and Fourier transform infrared results. Upon membrane surface modification using CNCs-capped AgNPs, bacterial growth on membrane surface was reduced. Specifically, the positive cohesion energy between the CNCs-capped AgNPs-modified PVDF membrane and thermophilic bacterial foulant was + 63.2 mJ/m2, distinctly proving reduced fouling. The findings were supported by 5.5 % flux decay of the modified membrane compared to 79.3 % flux decay of virgin PVDF membrane. This suggested a long-term membrane integrity in thermophilic bacterial contaminated feed solutions during the MD water desalination.