The implementation of an innovative office concept (e.g. open-plan, flexible workplaces and a paperless office concept) on health and productivity among office workers was evaluated with questionnaires of 138 workers at baseline and 6 and 15 months afterwards. Work-related fatigue, general health, change in health status, upper extremity complaints and perceived productivity were outcomes. No short-term significant differences were found in most outcomes except for quantity of performed work (decrease from 96% to 92%, p = 0.008). In the long-term, no significant differences were found in most outcomes except for an increase in general health (p = 0.011) and a decrease in prevalences of upper extremity complaints (33% to 22%, p = 0.021). Perceived productivity increased significantly 15 months after the implementation. It is concluded that innovative office concepts had no or limited effects on work-related fatigue, health changes and productivity but some positive effects on workers' general health and upper extremity complaints in the long term. Office innovation is being administered often but up to now seldom evaluated on workers' health and productivity.