Controlling the disinfection by-product (DBP) formation, while balancing the risk of bacterial contamination in finished water, requires an in depth understanding in both the chemistry of DBPs and the kinetic and mechanism of bacterial disinfection. Although numerous studies have examined different strategies on the reduction of DBP formation in finished waters, their main focuses are on natural organic matter (NOM) in source waters. Few studies evaluated the contributions of bacterial organic matter (BOM) on DBP formation. Breaking down of bacterial cells, releasing BOM into water, is an essential process in water disinfection. Prevalence of bacterial contamination in source waters and occurrences of biofilms in water treatment units and distribution systems are frequently reported. The contributions of organic matter from bacterial and microbial sources in drinking water treatment cannot be ignored. In this study, we compared the contributions of bacterial cells and humic acid (HA), under controlled laboratory environments, on the DBP formation from chlorination. We also evaluated the effects of HA, pH, and chlorine dosage on both disinfection efficiency and DBP formation. The results showed that bacterial cells are also potential DBP precursor. Presence of HA not only increased the DBP formation, but also decreased the disinfection efficiency of chlorination. pH and chlorine dosage also affect the disinfection efficiency and DBP formation of chlorination. High dosage of chlorine would increase both the disinfection efficient and DBP formation, while low pH increase the disinfection efficient with a lower DBP formation. The results suggest that high disinfection efficiency with low DBP formation of chlorination can be achieved by optimization of operation conditions. Based on our knowledge, this pioneering work is the first study to investigate the relationship between bacteria and DBP contaminations in water treatment processes at the same time.