In this study, chopping board meat samples collected from meat shops of Bharatpur Metropolitan City, Nepal, were screened for the presence of Escherichia coli (E. coli), with a special emphasis on the identification of extended-spectrum β-lactamase (ESBL)-producing strains. Representatives from the meat shops were also interviewed to understand the sanitary status and hygienic practices. E. coli bacteria were detected in one third (33/99) of the meat samples, while none of the samples had ESBL-producing strains. While 60.6% (60/99) of the meat shop personnel wore protective clothing, 15.15% (15/99) used gloves, and only 5.05% (5/99) had separate equipment for cleaning the viscera of animals. This study highlights the need for the regular screening of meat samples to identify pathogenic bacteria such as E. coli and for improvements in the sanitary status and hygienic practices of retail meat shops in Bharatpur Metropolitan City, Nepal.