Salmonella is a major cause of global gastroenteritis, with pig-based products being significant sources. The Hazard Analysis Critical Control Points (HACCP) standard ensures food safety by identifying Salmonella contamination dynamics and improving control strategies. A study in Thailand found that pork in HACCP-certified slaughterhouses had significantly reduced Salmonella contamination and antimicrobial resistance (AMR) compared to in non-HACCP facilities. However, both types of slaughterhouses still experience Salmonella contamination during the slaughtering process, with limited information available on contamination sources and critical steps. The current study compared Salmonella distribution and AMR profiles in two Thai pig slaughterhouses, one of which implemented HACCP. A total of 570 samples, including feces, carcass swabs, and environmental samples, were cultured for Salmonella and investigated for AMR. The overall prevalence was 24.7%, being significantly lower at the HACCP-compliant slaughterhouse 1 (S1, 13.7%) compared to the non-compliant slaughterhouse 2 (S2, 41.2%) (P = 0.03). Slaughterhouse-specific Salmonella prevalence varied across slaughtering steps, with S2 showing high contamination rates in carcasses post-final washing, persisting until post-cutting. Additionally, specific strains were found in various locations, including feces, carcasses, workers' hands, cutting boards, and knives before and during operations. Conversely, carcasses post-final washing in S1 had the lowest contamination. Real-Time PCR identified higher Salmonella contamination and a greater copy number in S2-cutting carcasses compared to in S1. Overall, 42.6% of isolates were multidrug-resistant, showing strong resistance to ampicillin and tetracycline, while 8.51% produced extended-spectrum beta-lactamase (ESBL). It is evident that continuous monitoring and control measures are crucial to mitigate contamination and antibiotic resistance in foodborne pathogens such as Salmonella. The current study confirms that adherence to HACCP in slaughterhouses significantly reduces Salmonella in pork products. However, contamination levels rose notably post-cutting in both HACCP and non-HACCP facilities, with equipment, other carcasses, and workers' hands acting as sources of contamination. Rigorous monitoring during cutting processes is essential to identify and mitigate contamination sources, thereby improving food safety in meat processing facilities.