The activated sludge (AS) process is widely applied in dyestuff wastewater treatment plants (WWTPs); however, the nitrogen removal efficiency is relatively low and the effluent does not meet the indirect discharge standards before being discharged into the industrial park's WWTP. Hence it is necessary to upgrade the WWTP with more advanced technologies. Moving bed biofilm processes with suspended carriers in an aerobic tank are promising methods due to enhanced nitrification and denitrification. Herein, a pilot-scale integrated free-floating biofilm and activated sludge (IFFAS) process was employed to investigate the feasibility of enhancing nitrogen removal efficiency at different hydraulic retention times (HRTs). The results showed that the effluent chemical oxygen demand (COD), ammonium nitrate (NH4+-N) and total nitrogen (TN) concentrations of the IFFAS process were significantly lower than those of the AS process, and could meet the indirect discharge standards. PCR-DGGE and FISH results indicated that more nitrifiers and denitrifiers co-existed in the IFFAS system, promoting simultaneous nitrification and denitrification. Based on the pilot results, the IFFAS process was used to upgrade the full-scale AS process, and the effluent COD, NH4+-N and TN of the IFFAS process were 91–291 mg/L, 10.6–28.7 mg/L and 18.9–48.6 mg/L, stably meeting the indirect discharge standards and demonstrating the advantages of IFFAS in dyestuff wastewater treatment.