Life cycle assessments of microalgal cultivation systems are often conducted to evaluate the sustainability and feasibility factors of the entire production chain. Unlike widely reported conventional microalgal cultivation systems, the present work adopted a microalgal-bacterial cultivation approach which was upscaled into a pilot-scale continuous photobioreactor for microalgal biomass production into biodiesel from wastewater resources. A multiple cradle-to-cradle system ranging from microalgal biomass-to-lipid-to-biodiesel was evaluated to provide insights into the energy demand of each processes making up the microalgae-to-biodiesel value chain system. Energy feasibility studies revealed positive NER values (4.95–8.38) for producing microalgal biomass but deficit values for microalgal-to-biodiesel (0.14–0.23), stemming from the high energy input requirements in the downstream processes for converting biomass into lipid and biodiesel accounting to 88–90% of the cumulative energy demand. Although the energy balance for microalgae-to-biodiesel is in the deficits, it is comparable with other reported biodiesel production case studies (0.12–0.40). Nevertheless, the approach to using microalgal-bacterial cultivation system has improved the overall energy efficiency especially in the upstream processes compared to conventional microalgal cultivation systems. Energy life cycle assessments with other microalgal based biofuel systems also proposed effective measures in increasing the energy feasibility either by utilizing the residual biomass and less energy demanding downstream extraction processes from microalgal biomass. The microalgal-bacterial cultivation system is anticipated to offer both environmental and economic prospects for upscaling by effectively exploiting the low-cost nutrients from wastewaters via bioconversion into valuable microalgal biomass and biodiesel.