Structural changes in the world of work are accompanied by changes in work content and working conditions, such as an increase in autonomy with respect to work tasks, working time and workplace. It is assumed that these aspects have a positive effect on health and satisfaction at work, but they may also blurry the boundaries of work and private lives and lead to self-endangering work behaviour. As leadership behaviour is particularly important for the safety and health of employees, we assume that it can also help to mitigate possible harmful effects of autonomy. Based on data from the European Working Conditions Survey, we found that working time autonomy and working from home are positively associated with temporal boundarylessness. The construct mediates the association between working from home and unfavourable health outcomes. With respect to working time autonomy, it only mediates the relationship with both health outcomes when constructive leadership is low. Thus, the two autonomy facets can be beneficial but might also deteriorate employees’ health by blurring the boundaries between private and work lives. In supporting employees by means of respect and guidance orientation and supporting employees, leaders can mitigate potentially detrimental effects of working time autonomy.