Fabrication of less-fouling and high performance membrane is essential to offer significant cost reductions in membrane bioreactor (MBR) processes. In this regard, nanodiamond (ND) embedded cellulose acetate (CA) nanocomposite membrane was prepared and characterized in a lab-scale submerged MBR system for treating of pharmaceutical wastewater. In order to achieve efficient dispersion and providing more hydrophilic property, NDs were functionalized via heat treatment method. Scanning electron microscopy (SEM), and contact angle measurements were used to determine the surface properties of membranes. To compare the nanocomposite membranes with a pure CA membrane, critical flux, fouling behavior, and anti-fouling properties against extracellular polymeric substances (EPS) were investigated. SEM images showed that in the presence of 0.5 wt% of functionalized ND nanoparticles, porous structure appears on the membrane surfaces. The obtained results showed that in presence of functionalized NDs; ND-COOH, surface hydrophilicity of nanocomposite membrane was much higher than that of pristine CA membrane. Higher critical flux was obtained by CA/ND-COOH (0.5 wt.% of NDs) nanocomposite membrane due to the change of surface characteristics. The filamentous bacteria in the MBR resulted in more foulants on the CA membrane surface, while less filamentous bacteria were attached on the CA/ND-COOH nanocomposite membrane. Analysis of extractable EPS showed that the concentrations of proteins and carbohydrates in the EPS and soluble microbial products (SMP) for CA/ND-COOH (0.5 wt.%) membrane are less than other membranes. Also, COD removal for all of the membranes was higher than 90%, whereas only 83.4% removal efficiency was reached in the activated sludge.