The coronavirus disease 2019 (COVID-19) outbreak began in China in December 2019, with the World Health Organization declaring a state of emergency in January 2020. Worldwide implementation of lockdown measures to slow the spread of the virus led to reduced physical activity, disrupted eating habits, mental health issues, and sleep disturbances, which increased the risk of lifestyle-related diseases such as metabolic syndrome (MetS). During the COVID-19 pandemic, healthcare workers, especially intensive care workers, experienced longer working hours and burnout, which further increased the risk of lifestyle-related diseases. Accordingly, it is important to identify individuals at a risk of new-onset MetS during a pandemic, which could direct preventive interventions. This study aimed to assess the heterogeneous impact of the COVID-19 pandemic on the incidence of new-onset MetS based on the conditional average treatment effect (CATE) and to identify at-risk populations. This study analyzed health checkup data obtained from Okayama University Shikata Campus workers using paired baseline and follow-up years. Baseline data encompassed 2017 to 2019, with respective follow-up data from 2018 to 2020. Furthermore, as the COVID-19 pandemic in Japan began in January 2020, workers who underwent follow-up health checkups in 2018 to 2019 and 2020 were considered as "unexposed" and "exposed," respectively. As the Shikata campus has several departments, comparisons among departments were made. The primary outcome was new-onset MetS at follow-up. Predictor variables included baseline health checkup results, sex, age, and department (administrative, research, medical, or intensive care department). X-learner was used to calculate the CATE. This study included 3,572 eligible individuals (unexposed, n=2,181; exposed, n=1,391). Among them, 1,544 (70.8%) and 866 (62.3%) participants in the unexposed and exposed groups, respectively, were females. The mean age (±standard deviation) of the unexposed and exposed groups was 48.2 ± 8.2 and 47.8 ± 8.3 years, respectively. The COVID-19 pandemic increased the average probability of new-onset MetS by 4.4% in the overall population. According to the department, the intensive care department showed the highest CATE, with a 15.4% increase. Moreover, there was large heterogeneity according to the department. The high-CATE group was characterized by older age, urinary protein, elevated liver enzymes, higher triglyceride levels, and a history of hyperlipidemia treatment. This study demonstrated that the COVID-19 pandemic increased the incidence of new-onset MetS, with this effect showing heterogeneity at a single Japanese campus. Regarding specific populations, workers in the intensive care department showed an increased risk of new-onset MetS. At-risk populations require specific preventive interventions in case the current COVID-19 pandemic persists or a new pandemic occurs.