The frequency and possible sources of non-starter lactic acid bacteria (NSLAB) and citrate fermenting bacteria (CFB) at four points of a milk supply chain were evaluated. The relationship between the distance from farms (G1 and G2) to industry with NSLAB, CFB and psychrotrophic bacteria populations was also evaluated. A positive correlation between psychrotrophic and CFB was verified, which points to the need for the correct use of good milking practices to control these bacteria. NSLAB showed a significant increase in the population in raw milk samples collected in industrial silos (4.4 log cfu mL−1). CFB populations showed a significant increase in milk from tank trucks (4 log cfu mL−1). There was no difference between G1 and G2 in microorganisms counts. Even after the pasteurisation process, NSLAB and CFB populations remained high, which points to the occurrence of post-heat treatment recontamination, formation of biofilms and/or the presence of thermoduric microbiota.