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Background: COVID-19 vaccine hesitancy in the United States is high, with at least 63 million unvaccinated individuals to date. Socioeconomically disadvantaged populations experience lower COVID-19 vaccination rates despite facing a disproportionate COVID-19 burden. Objective: To assess the factors associated with COVID-19 vaccine acceptance among under-resourced, adult patients. Methods: Participants were patients receiving care at a Federally Qualified Health Center (FQHC) in St. Paul, Minnesota. Data were collected via multiple modes over 2 phases in 2020 (self-administered electronic survey) and 2021 (study team-administered survey by telephone, self-administered written survey) to promote diversity and inclusion for study participation. The primary outcome was COVID-19 vaccine acceptance. Using logistic regression analysis, associations between vaccine acceptance and factors including risk perception, concerns about the COVID-19 vaccine, social determinants of health (SDOH), co-morbidities, pandemic-induced hardships, and stress were assessed by adjusted odds ratios (AORs) and 95% confidence intervals (CI). Results: One hundred sixty-eight patients (62.5% female; mean age [SD]: 49.9 [17.4] years; 32% <$20 000 annual household income; 69% <college education) were included in the study. Sixty-one percent of the patients received or were willing to receive the vaccine. Risk perception was positively associated with vaccine acceptance (AOR: 5.3; 95% CI: 2.5, 11.5, P  < .001), while concerns about the vaccine (eg, safety, side effects, rapid development of the vaccine, etc.) were negatively associated with vaccine acceptance (all P  < .001). SDOH, co-morbidities, pandemic-induced hardships were not associated with vaccine acceptance. Conclusions: Our study in a socioeconomically disadvantaged population suggests that risk perception is associated with an increased likelihood of vaccine acceptance, while concerns about the COVID-19 vaccine are associated with a lower likelihood of vaccine acceptance. As these factors could impact vaccine uptake, consistent, innovative, and context-specific risk communication strategies may improve vaccine coverage in this population.