The aim of this study was to investigate the effect of hazard analysis and critical control point (HACCP) system application on microbial hazard management levels of pork and manufacturing environments. In this study, we compared and analyzed microbial levels in raw meat, finished products, and manufacturing environments (knifes, gloves, and cutting boards) of HACCP and non-HACCP meat markets. In addition, we surveyed the hygiene statuses of HACCP and non-HACCP meat markets. The general bacterial counts in raw meat, finished products, and manufacturing environments were lower in HACCP meat markets than in non-HACCP meat markets. Particularly, non-HACCP meat markets exceeded the Ministry of Food and Drug Safety microbiological recommendation criteria for raw meats (8.7%) and finished products (8.7%). Escherichia coli and coliform counts in raw meat, finished products, and manufacturing environments were also lower in HACCP meat markets than in non-HACCP meat markets. The biological hazard levels of finished products from non-HACCP meat markets were affected by raw meat and manufacturing environment. Moreover, according to questionnaire survey results, personal hygiene, manufacturing environment, and facility standards were lower in non-HACCP meat markets than in HACCP meat markets. Implementation of HACCP at meat markets is expected to minimize food poisoning by reducing the biological hazard levels to provide safe livestock products to consumers.