The monitorization of carcass surfaces contamination along the slaughter lines enables the verification of the slaughter operations hygiene and the good manufacturing practices. Pork meat is a common source of human non-typhoidal salmonellosis, one of the most frequently reported foodborne illnesses worldwide. This study aimed to gather data on microbial loads in carcass surfaces in two slaughterhouses, before and after evisceration. Salmonella enterica search was made after evisceration, due to the frequent reference to pork as being a common carrier of this microorganism. The contamination of carcass surfaces was evaluated by delimitation of surface area with sterilized templates (100 cm2), and sampled by gauze swabs. Enumeration of total aerobic mesophilic microorganisms, Enterobacteriaceae, and Escherichia coli was performed. The detection of Salmonella was performed for carcass surfaces after evisceration, and from animal liver and floor drains (environmental). Significant differences (p < 0.05) were observed for mesophilic microorganisms, Enterobacteriaceae, and E. coli counts on the external surfaces, with higher counts after evisceration. The neck and abdominal area presented higher levels for mesophilic microorganisms, Enterobacteriaceae and E. coli, and a high prevalence of Salmonella. Salmonella was detected only in one of the studied slaughterhouses; 19 out of 259 analysed carcass samples were positive for Salmonella (7.3%). Salmonella was also detected in two livers and in two floor drains. A collection of 52 Salmonella isolates (44 from carcasses, 5 from livers, 3 from drains) was gathered. Three serovars of Salmonella were identified (Typhimurium 4,5:i- , Wernigerone and Derby), and 53.8% of isolates were multidrug-resistant. The results demonstrate the need for continuous improvement of slaughtering operations and good manufacturing practices, to ensure food safety of pork produced in Portugal.