Elevated costs of biomass downstream processing represent a severe limit to the industrial development of microalgal production systems. Biorefinery solutions allowing simultaneously deriving biofuels and extracting high value compounds must be explored to enhance economic feasibility. In this work, the possibility to extract carbohydrates, lipids and astaxanthin from a strain of Scenedesmus sp. is investigated. The analysis is mainly focused on analyzing the effect of consolidated procedures of extraction of carbohydrates and lipids on the degradation and recovery of astaxanthin. Microalgae were cultivated till achieving stationary phase and maintained in this phase to enhance lipids and astaxanthin accumulation. The fractions of total lipids, carbohydrates and astaxanthin of the produced biomass were 17 %, 33 % and 0.02 % respectively. No statistically significant difference in the astaxanthin content determined following Soxhlet extraction and a more gentle extraction method (Yuan et al. 2002) was found. The effect of transesterification conditions was also evaluated revealing a scarce degradation of astaxanthin in response to the achievement of elevated temperature, NaOH and dissolved oxygen concentrations. Reductions in astaxanthin content were in contrast obtained in response to the addition of H2SO4. These reductions were proportional to acid sample concentration. However a regeneration of astaxanthin was obtained by NaOH addition indicating reversibility of the degradation process. In accordance with these results, the possibility to perform biomass saccharification for carbohydrate extraction at progressively lower acid concentrations was investigated.