The increasing consumption of food supplements demands the development of improved analytical methodologies to ensure their quality and authenticity. In this paper, two new approaches, liquid chromatography coupled to mass spectrometry (LC-MS) and flow injection analysis-(electrospray ionization) mass spectrometry (FIA-(ESI)MS), were optimized and validated for their application in the quantitative analysis of bioactive S-allyl-L-cysteine (SAC) in commercial aged garlic supplements (AGS). Although both methodologies were found to be useful for the sensitive and precise quantitation of SAC, the LC-MS approach allowed the differential determination of SAC and its bioactive diastereoisomer, S-1-propenyl-L-cysteine (S1PC), together with the identification of a number of organosulfur compounds typical of garlic. Mass fingerprints by FIA-(ESI)MS were proposed as an advantageous alternative to LC-MS analysis when the fast (4 min/sample) screening of AGS for their SAC content is intended, as in applications aimed at high-throughput quality control or standardization. Finally, the results gathered by the application of these two methodologies evidenced the highly variable composition of commercial AGS, as well as the identification of a number of potential composition frauds affecting their genuineness and benefits on health.