Salmonella is a zoonotic foodborne pathogen that affects poultry health and reaches consumers through the food chain via contaminated products. A cross-sectional study was conducted to isolate and identify Salmonella and to detect antibiotic resistance genes in Salmonella isolates from retail meat shops in Chitwan, Nepal. The antimicrobial susceptibility test was carried out using the Kirby–Bauer disc diffusion method. Antibiotic resistance genes were detected by using multiplex polymerase chain reaction (PCR). A total of 216 samples, chicken meat (108) and water (108), were tested for the presence of Salmonella. Out of the 216 samples tested, 38 samples were positive, giving an overall prevalence of 17.59%. A higher prevalence of Salmonella was found in meat samples, 29.62% (32/108), compared with the water samples, 5.55% (6/108), which was statistically significant (p < 0.05). The antibiogram profile showed maximum resistance to doxycycline (88%), followed by tetracycline (86%), erythromycin (79%), ampicillin + sulbactam (76%), ceftriaxone (22%), levofloxacin (21%), gentamicin (18%), chloramphenicol (13%), and amikacin (15%). The prevalence of the tetB gene and ere(A) gene was 23.68% (9/38) and 18.42% (7/38), respectively, and the association was statistically non-significant (p > 0.05). However, mcr1, catA1, and blaTEM genes were not detected. The study recommends integrated surveillance encompassing human health, food safety, and animal health under the ‘One Health’ approach, highlighting the need for effective strategies involving poultry farms, retail meat shops, and consumers to minimize contamination and reduce the transmission of Salmonella along the food chain from primary production to consumption on a global scale.