In the last decade, microalgae cultivation has become an attractive solution for biomass valorisation. From an industrial standpoint, one important aspect is the combination of the mixotrophic growth of microalgae with the biosynthesis of fatty acids, which represents a sustainable feedstock for the biodiesel chain. Nevertheless, the actual energy-effectiveness of the whole process is doubtful as the indispensable biomass recovery and drying steps are energy-intensive. To discuss this issue, this work presents a comparison between a 3rd generation biodiesel production plant and a methanol synthesis facility, powered by photovoltaic (PV) electricity from sunlight. The objective is to evaluate the energy efficiency of the two production processes (by means of KPIs) given the same solar incidence area. The two process designs assume the best available technologies for the operations involved, in terms of reaction conversions and separation performances to maximise the yield in the final product.