Currently, astaxanthin demand is fulfilled by chemical synthesis using petroleum-based feedstocks. As such, alternative pathways of natural astaxanthin production attracts much research interest. This study aimed at optimising bioreactor operation parameters for astaxanthin production and evaluating strategies for its subsequent extraction. The effect of pH and agitation was evident, as a significant reduction in both biomass and astaxanthin production was observed when the culture pH was not controlled and a low agitation speed was applied. At controlled pH conditions and a high agitation speed, a significant increase in biomass (16.4 g/L) and astaxanthin production (3.6 mg/L) was obtained. Enzymatic yeast cell lysis using two commercial enzymes (Accellerase 1500 and Glucanex) was optimised using the central composite design of experiment (DoE). Accellerase 1500 led to mild cell disruption and only 9% (w/w) astaxanthin extraction. However, Glucanex treatment resulted in complete astaxanthin extractability, compared to standard extraction method (DMSO/acetone). When supercritical CO2 was employed as an extraction solvent in Accellerase-pre-treated Xanthophyllomyces dendrorhous cells, astaxanthin extraction increased 2.5-fold. Overall, the study showed that extraction conditions can be tailored towards targeted pigments present in complex mixtures, such as in microbial cells.