The aim of this work was to examine the effect of modified atmosphere packaging on the physicochemical and microbiological changes of Graviera Agraphon cheese during refrigerated storage. Blocks of Graviera Agraphon cheese weighing around 200 g were packaged under natural (control) or modified atmosphere packaging (MAP) conditions (50% N2 – 50% CO2) and stored at 4 °C or 10 °C for up to 85 d. Prior to packaging, groups of cheese blocks were inoculated with one each of the following foodborne pathogens at around 104 log cfu/g: Listeria monocytogenes, Salmonella Typhimurium, Escherichia coli O157:H7 or Staphylococcus aureus, whilst further groups of cheese blocks were not inoculated. The protein, fat, moisture and salt contents as well as the pH of control and MAP cheese samples did not change significantly (P > 0.05) throughout 4 °C storage, while the pH values of control and MAP cheese samples were significantly (P < 0.05) reduced at 10 °C storage. At 10 °C storage, yeasts and molds, psychrotrophs and lactic acid bacteria (LAB) were significantly higher (P < 0.05) for the normal atmosphere than the MAP cheese samples after the 4th, 8th and 4th days, respectively. At 4 °C storage, the yeasts and molds or psychrotrophs were significantly higher (P < 0.05) than those of control after the 6th and 15th days, respectively at 4 °C storage. All foodborne pathogens showed a higher decrease (P < 0.05) at 10 °C than 4 °C storage. S. aureus proved more sensitive in inactivation in the MAP conditions than atmospheric conditions. L. monocytogenes and S. aureus presented a higher decrease than that of E. coli O157:H7 and S. Typhimurium. In conclusion, MAP proved efficient in retarding the growth of yeasts, molds, psychrotrophs and E. coli O157:H7, L. monocytogenes, S. Typhimurium and S. aureus in Graviera Agraphon cheese during refrigerated storage at 4 and 10 °C.