Benzalkonium chloride (BAC) has been widely used as disinfectant in food processing, whereas there is still largely unknown concerning its profound and/or reverse effects on the pathogens control. This study was aimed to assess the effects of BAC disinfection on the controlling difficulty of foodborne pathogens, by investigating the growth rate, micromorphology, biofilm characteristics, and antibiotic resistance. The results showed that two pathogenic strains, identified as Proteus vulgaris PV29 and Bacillus cereus BC30, were residually remained on the processing utensils after BAC disinfection. Moreover, compared with the parent cells, the micromorphology of the subcutured cells under BAC stress changed, while final cell densities of P. vulgaris PV29 and B. cereus BC30 increased by 106 % and 18 %, respectively. In addition, the BAC-adapted cells formed more obvious and denser biofilms, within which the cell density doubled at most. Even worse, antibiotic resistance of the both strains to common antibiotics (including vancomycin, sulfamethoxazole, mezlocillin sodium, and minocycline) increased after prolonged BAC-adaption. In sum, the present study verified increased difficulty to control the foodborne pathogens of P. vulgaris PV29 and B. cereus BC30 with regular BAC disinfection, and enlighten future assessment on the potential risks of BAC disinfection.