Six naturally fermented (Greek-style) table olives of cultivars Itrana, Peranzana, Cellina di Nardò, Nocellara del Belice and Bella di Cerignola, as well as their corresponding brines, were studied by a combined strategy consisting of chemical, microbiological and molecular analyses. In particular, organic acids, sugars, polyphenols, fatty acids, biogenic amines and cultivable microbiota were detected by standard methods. Moreover, tyramine and histamine producing bacteria were evaluated by an original approach consisting of Reverse-Transcription (RT)-qPCR. At the end of the fermentation process, mesophilic lactobacilli and yeasts in brine represented the dominating biota, ranging from 6.25 to 7.84 log CFU/ml and from 6.5 to 7.56 log CFU/ml, respectively. Enterobacteriaceae and pathogens were undetectable in all the samples. In general, table olive preparations differed in chemical composition. In particular, C16:0 and C18:2c9,12 concentrations ranged from 9.9 to 18.8 % and from 5.4 to 15.4 % of total fatty acids, respectively. The main fatty acid detected was C18:1c9 while CLAc9, t11 was present only in traces. Polyphenol concentrations greatly differentiated the final product, depending on the cultivar. A low quantity of biogenic amines was found in some samples and biogenic amines producing bacteria were rapidly detectable by RT-qPCR.