Background: Presenteeism is affected by work-related and individual factors. Among individual factors, the effect of combining various lifestyle habits on presenteeism is unknown. Aims: This study aimed to determine the relationship between changes in multiple good lifestyle habits with a change in presenteeism and to examine the effect of psychological factors on this relationship. Methods: We performed a 1-year retrospective cohort study on employees of large Japanese companies. Data were collected from health check-ups and a self-administered questionnaire. Changes in presenteeism were measured using the Quality and Quantity method. Changes in lifestyle habits were measured using a modified form of Breslow's seven health practices. Psychological factors were measured using the Kessler 6-Item Psychological Distress Scale. Linear regression was used for statistical analysis. Results: The number of practised lifestyle habit changes was negatively correlated with a change in presenteeism. This result was consistent when adjusted for age, sex and company (B, -0.010; P < 0.05), but became non-significant when additionally adjusted for psychological distress (B, -0.006). When analysed separately, only an improvement in the body mass index (B, -0.054; P < 0.05) and a worsened sleep habit (B, 0.040; P < 0.01) influenced a change in presenteeism. Conclusions: This study suggests that improving various practised lifestyle habits in combination, rather than improving a single lifestyle habit, is beneficial in reducing presenteeism. Our finding that psychological distress altered the relationship of practised lifestyle habit changes with presenteeism indicates the importance of organizational-level intervention in presenteeism.