Effective separation of volatile fatty acids (VFAs), ammonia (NH4+-N) and reactive phosphorous (RP) generated from anaerobic fermentation liquid is critically important for efficient resource recovery. Flow-electrode capacitive deionization (FCDI) is proven to be capable of efficient removal of ions, environmentally friendly and cost-effective in operation. The performances of FCDI system in the separation of NH4+-N, RP, and acetate and mechanism of pHs and activated carbon on their performances were investigated. Results showed that a pH of 5.0 promoted the removal of NH4+-N (53.1 %) and RP (39.5 %), and 72.0 % of acetate was retained in the solution, which revealed that removal of NH4+-N and RP, and retention of acetate were evidently affected by speciation of ions. Furthermore, the recovery of NH4+-N and RP was undermined by the adsorption of ions on activated carbon. This study provides a novel insight of ion selective mechanism during the operation of the FCDI system.