High-pressure processing (HPP) has been used to control microorganisms and enzymes and avoid over-ripening in cheese. Excessive lipolysis is associated with over-ripening in cheese. However, little information about the effect of high pressure on microorganisms and lipolysis in mature cheese is available. For this reason, microbiological and lipolytic changes during refrigerated storage of pressurised Torta del Casar cheese (a raw ewe’s milk cheese) were studied. Mature cheeses (60 days of ripening) were high-pressure treated (200 or 600 MPa for 5 or 20 min) and stored at 6 °C. Cheese samples were analysed at day 60, just after high-pressure treatment, and during the refrigerated storage (at days 120, 180 and 240). Enterobacteriaceae counts were significantly reduced after high-pressure treatment, thus increasing the food safety of this cheese. In particular, Enterobacteriaceae showed a significant ( p < 0.01) decrease of 2.18 and 2.46 log units in cheeses treated at 200 MPa for 20 min at days 120 and 180, respectively; however, treatment at 600 MPa for 20 min only caused reductions of 2.09 and 1.79 log units at days 120 and 180. Free fatty acids content was not significantly influenced by high-pressure treatment, although it increased with time of storage.