Abstract Microalgae are renewable and promising feedstock rich in biochemicals for biofuel and bioenergy production. The viability of this technology relies on the energy- and cost-efficient cultivation (culture medium used) and harvesting (coagulant applied) processes. The natural coagulant of crystalline nanocellulose modified with 1-(3-aminopropyl) imidazole (CNC-APIm) was demonstrated as a green and recyclable coagulant for microalgal harvesting. However, optimisation is still needed to ensure its applicability to microalgae cultivated on wastewaters, no effect on biomass composition, as well as cost-effective harvesting. In this study, microalgal growth and nutrient removal capacity of Chlorella vulgaris (C. vulgaris) were first investigated on two types of municipal wastewaters. C. vulgaris grew well on both primary and 30% (v/v) diluted centrate wastewaters with biomass productivities of 0.071 ± 0.005 and 0.062 ± 0.006 g/(L·d), respectively. High nitrogen and phosphorus removal efficiencies (91.1–100%) were obtained. Subsequently, the wastewater-cultivated C. vulgaris was harvested using a novel natural coagulant of crystalline nanocellulose modified with 1-(3-aminopropyl) imidazole (CNC-APIm). Based on the optimization results of the Design of Experiments driven response surface methodology approach, the optimal conditions for maximum HEs (86.5%) and RCs (38.5 g-algae/g-CNC) responses were determined for C. vulgaris under the following conditions: 0.02 g-CNC-APIm/g-algae of mass ratio, 5 s of CO2 sparging time, 8 min of air sparging time, and 50 ml/min of air flow rate. Moreover, no statistically significant differences were observed in the contents of carbohydrate, protein, lipid and fatty acids in the biomass harvested by centrifugation and CNC-APIm, respectively, suggesting that CNC-APIm would not impact the downstream microalgal application. According to the rough technical and economical estimation, CNC-APIm will be an alternative to conventional coagulants for commercial microalgal harvesting application.