Introduction Noncommunicable diseases (NCDs) are still a major public health problem in Indonesia. Studies have shown that risk factors of NCDs are associated with coronavirus disease 2019 (COVID-19) severity and mortality. However, it is unclear whether NCD risk factors are also risks for new COVID-19 cases. This study aimed to obtain an NCD risk profile among university employees and its associations with contracting COVID-19. Methods A cross-sectional study was conducted in October 2021. Participants were administrative employees of Universitas Indonesia (UI), Depok City, West Java. Assessment of NCD risk factors was based on the World Health Organization STEPwise approach to NCD risk factor surveillance (WHO STEPS). Demographic, working, and medical-history data were obtained electronically by using a Google Form. Physical and laboratory examinations were done in the Integrated Post for NCDs. Risks were expressed as adjusted odds ratio (ORadj) and 95% confidence interval (CI) in multivariate analyses. Results A total of 613 employees were enrolled. Men were predominant (54.8%), and about 36% of them work in shift as security personnel. About 66.7% were overweight or obese and 77.8% had hypertension. There were 138 (22.8%) employees who had COVID-19. Nearly all (95.6%) had been fully vaccinated against COVID-19. At-risk waist circumference (ORadj 1.72, 95% CI 1.15-2.56, p = 0.008) and total cholesterol level of 200-239 mg/dL (ORadj 2.30, 95% CI 1.19-4.44, p = 0.013) were independent risk factors, but shift work (ORadj 0.52, 95% CI 0.34-0.80, p = 0.003) was protective against COVID-19. Conclusion The prevalence of NCD risk factors among university administrative employees was high, increasing the risk of contracting COVID-19. A behavioral intervention program to manage NCD risk factors at the university level is urgently needed according to the Health Promoting University framework.