Two batches of smoked, semi-hard (ripened for 45 d) San Simón da Costa cow's milk cheeses with Protected Designation of Origin were used to investigate the chemical, biochemical, and sensorial parameters that may be affected by modified-atmosphere packaging. Cheeses were packaged for 45 d as follows: vacuum packaging, packaging in 100% N(2), packaging in a gas mixture of 20% CO(2)/80% N(2), and packaging in a gas mixture of 50% CO(2)/50% N(2). The San Simón da Costa cheeses were characterized by high contents of lactic, oxalic, and citric organic acids. The main free amino acids found were isoleucine, phenylalanine, serine, valine, lysine, and glutamic acid, and the most abundant volatile compounds included ethanol, diacetyl, 2-butanol, isopropyl alcohol, furfural, acetaldehyde, 2-butanone, acetone, and 2-methylfuran. Modified atmospheres appeared to alter the ripening processes by affecting lipolysis, as indicated by the lower concentrations of butyric and propionic acids compared with control cheeses. In addition, modified-atmosphere packaging altered the proteolysis processes, yielding higher amounts of branched-chain alcohols. The results revealed that storage under modified atmosphere contributes to the accumulation of several compounds probably derived from smoke, including aldehydes such as 2-furancarboxaldehyde (furfural), alcohols such as 2-methoxyphenol (guaiacol), ketones such as 2-cyclopenten-1-one, and esters such as methyl furancarboxylate, which were negatively correlated with flavor. Vacuum packaging was the most useful technique in terms of preserving the sensory quality of San Simón da Costa Protected Designation of Origin cheeses. Considering the current demands for packaged portions of food at the distribution and retail levels and the potential health risks associated with some smoke-derived compounds usually present in some smoked foods, the results obtained in this study may be of special interest to the cheese industry.