Cross-contamination via equipment and the food-processing environment has been implicated as the main cause of Listeria monocytogenes transmission. The aim of this study, therefore, was to determine the occurrence and potential persistence of L. monocytogenes in 19 European cheese-processing facilities. A sampling approach in 2007–2008 included, respectively, 11 and two industrial cheese producers in Austria and the Czech Republic, as well as six Irish on-farm cheese producers. From some of the producers, isolates were available from sampling before 2007. All isolates from both periods were included in a strain collection consisting of 226 L. monocytogenes isolates, which were then typed by serotyping and pulsed-field gel electrophoresis (PFGE). In addition, metabolic fingerprints from a subset of isolates were obtained by means of Fourier-transform infrared (FTIR) spectroscopy. PFGE typing showed that six processing environments were colonized with seven persistent PFGE types of L. monocytogenes. Multilocus sequence typing undertaken on representatives of the seven persisting PFGE types grouped them into distinct clades on the basis of country and origin; however, two persistent strains from an Austrian and an Irish food processor were shown to be clonal. It was concluded that despite the fact that elaborate Hazard Analysis and Critical Control Point concepts and cleaning programs are applied, persistent occurrence of L. monocytogenes can take place during cheese making. L. monocytogenes sanitation programs could be strengthened by including rapid analytical tools, such as FTIR, which allow prescreening of potentially persistent L. monocytogenes contaminants.