The rapid depletion of fossil fuels and ever-increasing environmental pollution have forced humankind to look for a renewable energy source. Microalgae, a renewable biomass source, has been proposed as a promising feedstock to generate biofuels due to their fast growth rate with high lipid content. However, literatures have indicated that sustainable production of microalgae biofuels are only viable with a highly optimized production system. In the present study, a cradle-to-gate approach was used to provide expedient insights on the effect of different cultivation systems and biomass productivity toward life cycle energy (LCEA), carbon balance (LCCO) and economic (LCC) of microalgae biodiesel production pathways. In addition, a co-production of bioethanol from microalgae residue was proposed in order to improve the economic sustainability of the overall system. The results attained in the present work indicated that traditional microalgae biofuels processing pathways resulted to several shortcomings, such as dehydration and lipid extraction of microalgae biomass required high energy input and contributed nearly 21 to 30% and 39 to 57% of the total energy requirement, respectively. Besides, the microalgae biofuels production system also required a high capital investment, which accounted for 47 to 86% of total production costs that subsequently resulted to poor techno-economic performances. Moreover, current analysis of environmental aspects of microalgae biorefinery had revealed negative CO balance in producing microalgae biofuels.