BackgroundThis study analyzes the process of establishing and developing a cooperative vocational rehabilitation project with special focus on organizational and professional aspects. In the project, officials from the Swedish Social Insurance Agency and the Swedish Public Employment Service worked cooperatively with participants on long-term sick leave, youths with disability benefits, and people receiving social allowances. The officials used Motivational Interviewing (MI) as a method when meeting participants, and were able to offer flexible and tailored case management. The goal was to improve work ability and promote self-sufficiency.MethodsThe process evaluation was carried out through continuous data collection throughout the project (2012–2014), resulting in a total of 28 individual interviews and 17 focus groups with officials and managers. The material was categorized through an inductive content analysis, and analyzed using social capital as a theoretical frame.ResultsThe evaluation points to how issues related to design, organization and management contributed to the project not reaching its goals, e.g. problems with recruitment of participants, the funding structure, and staffing problems on the managerial level. Still, officials reported positive effects of close cooperation, which was perceived as facilitating the case management by fostering a mutual understanding and access to resources and rehabilitation measures from more than one authority.ConclusionsCooperative work combined with the use of MI and flexible case management seem to promote an increased trust between officials from different authorities and participants, which in the study is conceptualized as bonding and bridging social capital (between officials) and linking social capital (between officials and participants). The organizational problems combined with the relatively large differences in approaches between the project and regular practice obstructed implementation, where the authorities involved did not appear to be ready for implementing methodologies that require organizational restructuring.Electronic supplementary materialThe online version of this article (doi:10.1186/s12889-017-4357-x) contains supplementary material, which is available to authorized users.