In this research, silver/graphene oxide (Ag/GO) nanohybrid was first synthesized and used in production of polysulfone (PSF) ultrafiltration (UF) membranes via phase inversion method for concentrating phycocyanin (PC) and treating methylene blue (MB) dye effluent. Designing the experiment (DOE) using Box-Behnken method by Design Expert software helped to calculate the optimal values of the variables under study. The studied variables included PSF polymer concentration, polyvinyl pyrrolidone (PVP) pore-former concentration and Ag/GO nanohybrid content, which were investigated for their effects on pure water flux (PWF) and MB pigment rejection. According to the results of the DOE, the membrane containing 19.485 wt% PSF, 0.043 wt% PVP and 0.987 wt% Ag/GO was selected as the optimal membrane. Due to the high price of PC as drug, and the importance of removing MB pigment from the effluent of dyeing and textile industries, the membranes were first optimized with MB pigment and then the optimal membrane was used for concentrating PC. The results showed that PWF reaches from 40.05 L.m− 2.h− 1 (LMH) for the neat membrane to 156.73 LMH for the optimized membrane, which shows about 4 times improvement. Compared to the neat membrane, flux recovery ratio (FRR) of the optimized membrane increased by about 20% and its total fouling (Rt) decreased by about 10%. Also, the results showed that the optimized membrane can remove 81.6% of MB, as well as to reject 93.8% of PC.