Microalgae are considered a promising feedstock of biomass for the production of biofuels. The capacity of some strains to accumulate lipids makes them an interesting alternative for biodiesel production. The anaerobic digestion of the spent (lipid-extracted) biomass has been proposed as a way to increase energy yield and sustainability of bioenergy production from microalgae. Anaerobic digestion would produce biogas, but also would provide conditions for nutrients recovery. Present research was oriented to determine potential contribution of anaerobic digestion of spent biomass to biodiesel production from microalgae. Two microalgae species were considered in this study, Botryococcus braunii and Nannochloropsis gaditana. Bio-methane potential tests revealed methane yields of 407 and 450 mL CH4/gVS for B. braunii and N. gaditana, respectively. Latter values represent 56 and 61% of total energy in spent microalgae, measured as calorific potential. Mass and energy balances for biodiesel and biogas production indicate that close to 14% of the energy contained in the biomass could be transferred to biodiesel. When biogas is also produced, potential energetic yield of both biofuels would increases to close to 55%. Energy balances of a potential biodiesel and biogas production indicate that traditional harvesting methods such as centrifugation and the inclusion of a biomass drying step process would yield negative energetic balances, even when biogas and biodiesel are both produced. Thus, future research efforts should focus on the development of low energy harvesting methods and in alternatives for biomass processing circumventing biomass drying.