Background Although coronavirus disease 2019 is causing a variety of psychological problems for workers, there are few longitudinal studies on changes in workers’ mental health by workplace intervention. This study aimed to evaluate the change in the prevalence of depression and anxiety according to the active involvement of the workplace. Methods This study was conducted on 1,978 workers at a workplace who underwent a health screening from January 2019 to August 2020, and classified depression and anxiety disorders using a self-report questionnaire. After the first pandemic, the company stopped health screening, took paid leave and telecommuting, and conducted interventions such as operating its own screening clinic. To see if this workplace intervention affects workers’ mental health, we conducted generalized estimating equations to compare odds ratio (OR). Results In the pre-intervention group, 384 people (16.86%) had depression, and 507 people (22.26%) had anxiety disorder. Based on the OR before intervention, the OR of depression decreased to 0.76 (0.66–0.87) and the OR of anxiety disorder decreased to 0.73 (0.65–0.82). Conclusions As a result of this study, it was confirmed that workplace intervention was related to a decrease in depression and anxiety. This study provides basic data to improve workers’ mental health according to workplace intervention, and further research is needed according to workplace intervention in the future.