Microalgae have been envisioned as a key resource for use as a transportation biofuel. However, microalgae cultivation on a mass scale is associated with several challenges, including production cost and desired quality. In the quest for high-density microalgae cultivation having desired traits applicable to biofuel quality, the present work aimed to evaluate microalgae cultivation systems systematically. Column photobioreactor (PBR) and microalgal-biofilm reactor (MBR) were selected for microalgae cultivation as a suspended culture and as a biofilm, respectively. Microalgae Chlorella pyrenoidosa was grown under mixotrophic mode in laboratory-controlled conditions at an illumination of 15,000-20,000 Lux, a temperature of 25±2°C, and a light/dark cycle of 16/8 hours. The selected microalgae was cultivated in domestic wastewater supplemented with glycerol. The cultivation systems were evaluated in terms of biomass growth, biochemical composition, and quality of biofuels. As a result, MBR was observed to achieve the maximum biomass productivity of 10 g m-2 d-1. In contrast, in PBR, biomass productivity of 3 g m-2 d-1 was attained. The MBR-grown biomass had a higher carbohydrate fraction than PBR-grown biomass. On the other hand, the lipid content for PBR grown biomass was slightly higher than the MBR-grown biomass. Further, the biodiesel based on PBR-grown biomass showed quality in agreement with international standards (ASTM D6751-02, EN14214). In contrast, the case was not the same for microalgae cultivated in MBR. The results showed microalgae cultivation as a suspended culture in PBR was appropriate for biodiesel production. Similarly, the MBR-grown biomass can be directed for biogas or bioethanol production. Therefore, during the selection and scale-up of the microalgae cultivation system, a thorough investigation of biofuel quality along with biomass productivity and biochemical composition is suggested.