Lipids of microalgae as well as residues of diverse origins are considered currently among the most favourable raw materials to be transformed into liquid biofuels, due reduced ambient impacts. This study highlights the effect of molasses and ammonium acetate, as carbon and energy, on synthetic domestic wastewater (SDW) as a culture medium for lipids synthesized by Scenedesmus sp. (SCRE-1) and their potential as biofuels after being processed through transesterification (TE) or hydrodeoxygenation (HDO) reactions.It was found that biomass and lipid production from SDW-molasses was higher than those from ammonium acetate. Most of the lipids (79.4 ± 0.310 %) produced in this case, were capable of being transesterified into esters obtaining a high-quality biodiesel (BD). The remaining lipids were unesterifiable, thus requiring another transformation route to become useful biofuels. When the whole lipids (not only the unesterifiable potion) from SDW-molasses culture were processed via HDO reaction, high-quality green diesel (GD) was obtained as the main product, accounting for 96.4 ± 0.376 % of the chromatographic area.On the other hand, lipids generated from SDW-ammonium acetate allowed the formation of 22.0 ± 0.086 % of medium quality BD through TE reaction, 2.5 ± 0.010 % of a good quality GD was also formed, while 75.6 ± 0.295 % of the lipids required another thermochemical rout different from TE to become useful biofuels. After processing the lipids though the HDO reaction, 44.1 ± 0.172 % of high-quality BJ, 17.4 ± 0.068 % of poor-quality GD, and 33.9 ± 0.132 % of poor-quality BD were obtained. These results indicate that the production of lipids from the microalgae Scenedesmus sp. (SCRE-1) cultivated in SDW is a promising option for obtaining high-quality liquid biofuels though TE reaction but mainly through HDO reaction.