“Pera Rocha do Oeste” is a pear (Pyrus communis L.) variety native from Portugal with a Protected Designation of Origin (PDO). To supply the world market for almost all the year, the fruits are kept under controlled storage. This study aims to identify which classical physicochemical parameters (colour, total soluble solids (TSS), pH, acidity, ripening index, firmness, vitamin C, total phenols, protein, lipids, fibre, ash, other compounds including carbohydrates, and energy) could be fingerprint markers of PDO “Pera Rocha do Oeste”. For this purpose, a data set constituting fruits from the same size, harvested from three orchards of the most representative PDO locations and stored in refrigerated conditions for 2 or 5 months at atmospheric conditions or for 5 months under a modified atmosphere, were selected. To validate the fingerprint parameters selected with the first set, an external data set was used with pears from five PDO orchards stored under different refrigerated conditions. Near infrared (NIR) spectroscopy was used as a complementary tool to assess the global variability of the samples. The lightness of the pulp; the b* CIELab coordinate of the pulp and peel; and the pulp TSS, pH, firmness, and total phenols, due to their lower variability, are proposed as fingerprint markers of this pear.