In the United States, obesity has increased in prevalence over time and is strongly associated with subsequent outcomes such as diabetes mellitus (DM) and nonalcoholic fatty liver disease (NAFLD). It is unclear, however, as to how the magnitude of NAFLD risk from obesity and DM is increased in safety-net health system settings. Among the San Francisco Health Network (SFHN) patients (N = 47,211), we examined the association between Body Mass Index (BMI) and elevated liver enzyme levels, including interaction by DM status. Our findings revealed that 32.2 percent of SFHN patients were obese, and Pacific Islanders in the safety-net had the highest rates of obesity compared to other racial groups, even after using higher race-specific BMI cutoffs. In SFHN, obesity was associated with elevated liver enzymes, with the relationship stronger among those without DM. Our findings highlight how obesity is a stronger factor of NAFLD in the absence of DM, suggesting that practitioners consider screening for NAFLD among safety-net patients with obesity even if DM has not developed. These results highlight the importance of directing efforts to reduce obesity in safety-net health systems and encourage researchers to further examine effect modification between health outcomes in such populations.