The present work studied and compared the low-cost carbon sources SCM and CPS as feedstocks for carotenoid and lipid production by the oleaginous yeast R. toruloides NCYC 921 using multiparameter flow cytometry. For the first time, this at-line technique was used to assess the yeast carotenoid content and cell viability of the cells grown on these complex substrates in a fast way, which is not possible when using traditional analytical methods for process monitoring.