Sampling approaches following the dairy chain, including microbiological hygiene status of critical processing steps and physicochemical parameters, contribute to our understanding of how Staphylococcus aureus contamination risks can be minimised. Such a sampling approach was adopted in this study, together with rapid culture-independent quantification of Staph. aureus to supplement standard microbiological methods. A regional cheese production chain, involving 18 farms, was sampled on two separate occasions. Overall, 51·4% of bulk milk samples were found to be Staph. aureus positive, most of them (34·3%) at the limit of culture-based detection. Staph. aureus positive samples >100 cfu/ml were recorded in 17·1% of bulk milk samples collected mainly during the sampling in November. A higher number of Staph. aureus positive bulk milk samples (94·3%) were detected after applying the culture-independent approach. A concentration effect of Staph. aureus was observed during curd processing. Staph. aureus were not consistently detectable with cultural methods during the late ripening phase, but >100 Staph. aureus cell equivalents (CE)/ml or g were quantifiable by the culture-independent approach until the end of ripening. Enterotoxin gene PCR and pulsed-field gel electrophoresis (PFGE) typing provided evidence that livestock adapted strains of Staph. aureus mostly dominate the post processing level and substantiates the belief that animal hygiene plays a pivotal role in minimising the risk of Staph. aureus associated contamination in cheese making. Therefore, the actual data strongly support the need for additional sampling activities and recording of physicochemical parameters during semi-hard cheese-making and cheese ripening, to estimate the risk of Staph. aureus contamination before consumption.