The aim of this study was the chemical, microbiological, textural, and sensory characterization of pilot-scale prototypes of an Italian ewe’s raw milk cheese (Caciofiore) curdled with commercial Cynara cardunculus rennet, used as a control, and crude extracts obtained from flowers of either spontaneous or cultivated Onopordum tauricum. Hence, the control and experimental cheese prototypes produced in two rounds of cheesemaking trials were assayed, at the end of their 60-day maturation, for the following features: pH, titratable acidity, dry matter, fat, total and soluble nitrogen (TN and SN, respectively), ash, salt, protein, lactose, viable plate counts and composition of the bacterial and fungal populations, color, texture, volatile organic compounds (VOCs), and olfactory attributes by sensory analysis (the latter for the sole prototypes curdled with the commercial rennet and the extract obtained from cultivated O. tauricum). The data overall collected showed a very low impact of the type of thistle rennet on the analyzed cheese traits, with significant differences being exclusively found for SN/TN%, titratable acidity, color, and adhesiveness. By contrast, a higher impact of the cheesemaking round was seen, with significant differences being observed for salt content, load of presumptive lactobacilli, thermophilic cocci, and Escherichia coli, and levels of the following VOCs: 2,3-butanedione, 2-pentanone, 1-butanol, 2-heptanone, 3-methyl-1-butanol, 2-heptanol, 2-nonanone, dimethyl trisulfide, 2-methyl propanoic acid, butanoic acid, and 3-methyl butanoic acid. Sensory analysis revealed a strong ewe’s cheese odor, accompanied by other olfactory notes, such as pungent, sour curd, sweet, and Parmesan cheese-like notes, in all the analysed cheese prototypes. Moreover, key odor active compounds, including butanoic acid, ethyl butanoate, 2,3-butanedione, 1-octen-3-one, and dimethyl trisulfide, were identified by GC-olfactometry analysis. Regarding the odor attributes as determined by sensory analysis, again the type of rennet had an almost negligible impact, with significant differences being only perceived for 1 or 2 out of 20 odor attributes, depending on the analytical conditions applied. Although some aspects deserve further investigation, the results herein collected confirm that O. tauricum can be regarded as an alternative source of thistle rennet for the manufacture of Caciofiore cheese, and more in general, Mediterranean ewe’s milk cheeses.