Microalgae bio-treatment of synthetic fertilizer wastewater is particularly attractive due to their photosynthetic capabilities. Microalgae tend to convert solar energy into useful biomass, incorporating with the nutrients that present in wastewater, such as nitrogen and phosphorus. However, harvesting of microalgae remains a challenge because of the small size (3–30 μm) of microalgae cells and the repulsion between the negatively charged microalgae cells maintains a stable cell suspension. Magnetic-aided-embedding-flocculation strategy, which is one-step method by mixing microalgae, magnetic particles and flocculant together, is proposed for microalgae harvesting in order to meet cost and time effectiveness. In this study, the optimum cell separation efficiency of Chlorella vulgaris microalgae above 96% at 5 mg/L of chitosan dosage is achieved. With the aid of iron oxide particles, either micro- or nano-size, the sedimentation rate of cell flocs up to 250 cm/h is obtained when 10 mg/L of iron oxide is embedded into the cell flocs. The sedimentation rate with the embedding of iron oxide shows about 2 times faster than that of without magnetic particles. This strategy had proven effective for the polishing of the pretreated synthetic fertilizer wastewater by removing up to 53%, 74% and 70% of ortho-phosphate, nitrate and ammoniacal nitrogen, respectively. In addition, the presence of iron oxide particles and chitosan in microalgae harvesting that showed no adverse effect toward the quantity and quality of extracted lipid. This strategy is proven feasible for fertilizer wastewater treatment and biodiesel production. [ABSTRACT FROM AUTHOR]