Aims: To investigate the sources of Salmonella spp. in Alheira and how to trace it, by studying the way that Salmonella spp. is distributed across production lines, by applying multifactorial correspondence analysis to occurrence data, and through the use of polymerase chain reaction (PCR) molecular typing methods. Methods and Results: Four production lines, four batches of Alheira and 14 sampling sites were analysed over four sampling periods. Eighty-five Salmonella spp. isolates were obtained from the 896 microbial analyses performed. The basic occurrence analysis values, multiple correspondence analysis and PCR molecular typing methods confirmed that the presence of Salmonella spp. in Alheira was directly related to it being present in casings. Results obtained from PCR molecular typing added a measure of detail, highlighting potential cross-path contamination caused by contaminated surfaces. Conclusions: The presence of Salmonella spp. in Alheira was a result of the use of contaminated casings, as well as cross-path contamination caused by contaminated surfaces. An analysis of the occurrence data indicated that these casings were the source of Salmonella spp. contamination in Alheira. PCR molecular typing methodology, which is known to have a greater discriminatory power and tracing capacity, indicated the presence of cross-path contamination. Significance and Impact of this Study: Increased awareness of Salmonella spp. contamination sources and their spread across the production line helps shape the development of new strategies for controlling this pathogen.