The aim of this study was to assess the hygienic quality of raw milk used in the manufacture of São Jorge, a Protected Denomination of Origin Portuguese semihard cheese, as well as to ascertain the sanitary conditions prevailing during its processing. Viable counts of Enterobacteriaceae and Micrococcaceae were accordingly obtained, pertaining to 21 independent batches (including samples of raw milk, curd, and cheeses after 1, 3, and 4 months of ripening), from 7 dairy farms. Standard plate counts (log CFU per milliliter or per gram) ranged from 6.1 to 8.6 in raw milk, whereas they ranged from 7.0 to 8.0 in 4-month-old cheeses. Viable counts of Enterobacteriaceae ranged between 5.9 and 7.0 in raw milk and between 0.0 and 1.3 in 4-month-old cheeses. Species identified within this family encompassed Klebsiella oxytoca, Klebsiella cloacae, Klebsiella pneumoniae, Enterobacter sakazakii, and Escherichia coli; Klebsiella ornithinolytica, Klebsiella terrigena, and Serratia odorifera were detected only in raw milk. No Salmonella whatsoever could be detected in any of the samples. Viable counts of Micrococcaceae ranged between 4.7 and 5.9 and between 1.3 and 3.3 in raw milk and 4-month-old cheeses, respectively. Species identified within this family encompassed Staphylococcus sciuri, Staphylococcus epidermidis, Staphylococcus saprophyticus (which was found mainly in ripened cheeses), and Staphylococcus aureus (which was not detected in 4-month-old cheeses). Accompanying physicochemical analyses included determination of moisture, salt, and pH. Statistical analyses revealed a negative correlation between salt content and viable numbers of Enterobacteriaceae in cheese, whereas in the case of Micrococcaceae, a more negative correlation was found between viable numbers and moisture content than between viable numbers and pH. The results of our study indicate, in general, poor milk handling conditions in all farms, given that the indicators total mesophile and Enterobacteriaceae counts were high, between 100- and 1,000-fold those enforced by international standards pertaining to the matrices in question. However, by the time of regular consumption (i.e., after 4 months of ripening), São Jorge cheeses exhibit low levels of contamination by Enterobacteriaceae and S. aureus, as well as absence of Salmonella.