Edelfosine is a lysophosphatidylcholine analogue and the prototype of a new class of compounds being investigated for their potential as highly selective chemotherapeutic agents. Edelfosine has been implicated as affecting numerous different metabolic pathways, though its mechanism of action is not well understood at this time. To gain further insight into edelfosine’s mechanism of action we carried out mass spectrometry based metabolomic and lipidomic profiling of yeast exposed to a cytostatic concentrations of edelfosine. Using multivariate projection methods and statistical analysis, we determined that edelfosine exerts a significant effect on many aspects of yeast metabolism. Metabolic pathways that were found to be perturbed included those involved with amino acid metabolism, sugar metabolism, the TCA cycle, fatty acid biosynthesis, sphingolipid metabolism, glycerophospholipid metabolism and glycerolipid metabolism. It was also observed that there is a kinetic difference in the response of polar and non-polar metabolites to edelfosine treatment in yeast.