Flexible work arrangements are common worldwide, but knowledge on how to achieve a sustainable work environment is sparse. The aim of this study was to use a participatory approach to identify concrete suggestions and key areas for improvement that were considered relevant, effective, and feasible for promoting good work environment and health at organizational, work group and individual level (O-G-I), among office employees with flexible work arrangements. Eight focus group interviews (including 45 employees) were conducted in a large Swedish government agency in 2017. By using a Tree diagram approach, employees made a total of 279 suggestions for improvements, which were sorted into O-G-I levels and mapped into 18 key areas. We found that 13 key areas addressed organizational level (e.g., improving leadership, policy, job demands, and work efficiency), two key areas addressed group level (create common rules of availability and activity-based working), and three key areas addressed individual level (e.g., individuals’ responsibility to clearly communicate their availability). The participatory process was effective in obtaining concrete suggestions and key areas in need of improvement, which may provide an action plan that can guide organizations in developing interventions to promote good work environment and health in flexible work.