In this study, a well-controlled three-stage process was proposed for high ammonium removal from synthetic wastewater using selected promising microalgal strain UMN266. Three trophic modes (photoautotrophy, heterotrophy, and mixotrophy), two N sufficiency conditions (N sufficient and N deprived), two inoculum modes (photoautotrophic and heterotrophic), and different NH4+-N concentrations were compared to investigate the effect of trophic mode conversion and N deprivation on high NH4+-N removal by UMN266. Results showed that photoautotrophic inoculum with trophic mode conversion from heterotrophy to photoautotrophy and N deprivation in Stage 2 turned was the optimum plan for NH4+-N removal, and average removal rates were 12.4 and 19.1 mg/L/d with initial NH4+-N of 80 and 160 mg/L in Stage 3. Mechanism investigations based on algal biomass carbon (C) and N content, cellular composition, and starch content confirmed the above optimum plan and potential of UMN266 as bioethanol feedstock. (C) 2015 Elsevier Ltd. All rights reserved.