Aquaculture bioflocs is an agglomeration of organic matter and microorganisms in the aquaculture system. The bioflocs is capable of controlling water quality through absorption of undesirable nutrients in wastewater. It also contains microalgae such as Chlorella sp. that can be harvested for use in aquaculture applications. Nevertheless, the current harvesting technologies are based on chemicals or expensive membrane filtration. This study investigated the utilization of chitosan as a natural bio-coagulant to harvest Chlorella sp. with an emphasis on the coagulation–flocculation efficiency. The optimum dosage of chitosan at 30 mgL−1 achieved 98% of microalgae removal efficiency and 80% of biomass recovery. The treated water was safe within a neutral pH level with less than 5 NTU of turbidity. The results show that chitosan can be an alternative and environmental-friendly bio-coagulant for microalgae harvesting. •Microbial composition of bioflocs is 35% bacteria, 29% microalgae, 24% fungi, 12% zooplankton.•Bioflocs has the ability to treat nutrient of aquaculture wastewater within 21 days of formation.•Chlorella sp. was the most dominant microalgae in bioflocs.•Optimum dosage of chitosan was 30 mg L−1 with high removal efficiency, biomass recovery, and low turbidity.