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Valdeón cheese is a Spanish Protected Geographical Indication of blue‐veined cheese produced on an industrial scale from raw or pasteurised cow and/or goat milk. The aim of this work was to evaluate the impact of pasteurisation on the microbiological, physicochemical and sensory characteristics of cheese. Cheeses made with raw milk showed higher counts of lactobacilli and enterococci, as well as lower values of pH and D‐lactic acid and salt/moisture ratio. Cheeses made with pasteurised milk showed greater extent of proteolysis, higher concentration of free amino acids and lower concentration of biogenic amines. Pasteurisation produced more elastic and harder cheeses, but with a lower sensory profile.