The purpose of the current study was to find farm-level factors influencing the bacteriological prevalence of Yersinia enterocolitica in pigs at time of slaughter. On 100 farms, data concerning a broad range of farm aspects (e.g., management and housing system, biosecurity, and hygiene measurements) were collected using a face-to-face questionnaire. At the slaughterhouse, tonsils of on average 70 slaughter pigs per batch were sampled to determine the infection status of pigs. After univariable mixed-effect logistic regressions, variables that were related to the Yersinia prevalence (p<0.05) were included in a multivariable model. In this model, the factors remaining positively associated with a higher Y. enterocolitica carriage in the tonsils (p<0.1) were an increasing number of piglet suppliers, a high density of pig farms in the area, and the use of semislatted floors in the fattening pig unit. The proper use of a disinfection bath before entering the stables and a poor biosecurity level were protective factors, although a higher prevalence was associated with a significant positive interaction between the presence of pets in the stables and a poor biosecurity level. Reducing the number of piglet suppliers, using a disinfection bath properly, and prohibiting pets inside the stables could be easily implemented by pig farmers to lower the prevalence of Y. enterocolitica in pigs at slaughter.