Yersinia enterocolitica is an important foodborne pathogen that is primarily transmitted to humans through the consumption of contaminated pork. Different matrices of pigs at slaughter were tested for the presence of human pathogenic types of Y. enterocolitica using direct plating, selective enrichment, and cold enrichment. Y. enterocolitica serotype O:3 was isolated from the tonsils and faeces of 55.3% and 25.6% of pigs, respectively. The pathogen was also recovered from 15.0% of swab samples taken from the carcass surface post-evisceration. Tonsils positive by direct plating revealed an average concentration of 3.99 log10 Y. enterocolitica per gram, whereas the majority of positive faecal and carcass samples were contaminated below the detection limit of enumeration. The relative sensitivity of the methods to recover pathogenic Y. enterocolitica varied among the different matrices. Nevertheless, cold enrichment was significantly more efficient than direct plating and selective enrichment for all three sample matrices. From the 2082 recovered Y. enterocolitica isolates, 1742 (83.7%) harboured the virulence plasmid. Isolates obtained from faeces were more likely to contain the virulence plasmid than isolates from tonsils and carcass swabs. To obtain reliable results regarding the presence of plasmid-carrying Y. enterocolitica isolates, sensitive isolation methods should be combined with testing of a sufficient number of isolates.