The phosphate (P) fertilizer industry generates a highly hazardous and acidic wastewater. The present study reports the evaluation of an integrated precipitation and Enhanced Biological Phosphorus Removal (EBPR) process for the treatment of fertilizer plant wastewater and effluent detoxification, assessed by microtoxicity and seed germination tests. Effluent samples were collected from a local P fertilizer industry and were characterized by their high fluoride and P content. First, the samples were pre‐treated by precipitation of P and fluoride ions using hydrated lime. The resulting low‐fluoride and phosphorus effluent was then treated with the EBPR process to monitor the simultaneous removal of carbon, nitrogen, and phosphorus. Phosphorus removal included a two‐stage anaerobic/aerobic system operating under continuous flow. Pre‐treated wastewater was added to the activated sludge and operated for 160 days in the reactor. The operating strategy included increasing the organic loading rate from 0.3 to 1.2 g chemical oxygen demand (COD)/L day. The stable and high removal rates of COD, NH4+‐N, and PO43−‐P were then recorded. The mean concentrations of the influent were approximately 3600 mg COD/L, 60 mg N/L and 14 mg P/L, which corresponded to removal efficiencies of approximately 98%, 86%, and 92%, respectively. The microtoxicity of the treated wastewater was then monitored by LUMIStox and its phytotoxicity was investigated on cress, tomato, wheat, maize, ryegrass, and alfalfa seed germination. LUMIStox tests showed that treatment allowed a significant toxicity removal. Moreover, the untreated wastewater inhibited the species germination even when diluted 10 times, whereas a positive effect of treated wastewater was noticed. © 2013 American Institute of Chemical Engineers Environ Prog, 33: 463–471, 2014