Antibiotic-resistant bacteria in poultry meat are a threat to public health. In this study, we compared the Enterococcus spp. loads and antibiotic-resistance profiles between carcasses of conventionally and organically raised chickens. A total of 144 chicken carcasses (72 conventional and 72 organic) was collected from local retail markets in Seoul, South Korea. Overall, 77.7% (112 of 144; 75% conventional and 80% organic) of chicken carcasses were positive for Enterococcus. The mean loads of Enterococcus spp. were greater in conventional chicken carcasses, at 2.9 ± 0.4 log CFU/mL, than those in organic chicken carcasses, at 1.78 ± 0.3 log CFU/mL (p < 0.05). A total of 104 isolates (52 from conventional and 52 from organic chicken carcasses) was randomly selected for further analysis. The predominant species was Enterococcus faecalis in both conventional and organic chicken carcasses (57.7 and 76.9%, respectively; P > 0.05). Rates of resistance to ciprofloxacin and erythromycin, which are used in veterinary medicine in South Korea, were significantly higher in conventional chicken carcasses than in organic chicken carcasses. However, we found no difference between the rates of resistance to antibiotics such as vancomycin and tigecycline, which were not registered for use in veterinary medicine in South Korea, of Enterococcus isolates from conventional and organic chicken carcasses. In addition, although multidrug resistant isolates were obtained from both types of chicken samples, the prevalence of samples positive for Enterococcus was significantly higher in conventional chicken carcasses than in organic chicken carcasses (P < 0.05). The most common multidrug resistance pattern was erythromycin-tetracycline-rifampicin in conventional chicken carcasses and quinupristin-dalfopristin-tetracycline-rifampicin in organic chicken carcasses. A high level of gentamicin resistance was observed in isolates from not only conventional (5.8%) but also organic chicken (1.9%) carcasses, with no significant difference in rates between them (P > 0.05). Despite this, our results suggest that organic food certification is effective in reducing fecal contamination and the burden of antibiotic-resistant Enterococcus spp. in chicken carcasses.