The Rural Research Capacity Building Program commenced in 2006 with the aim of developing research skills in rural health workers. The program was based on the capacity building principles of workforce development, organisational development, resource allocation, partnership and leadership. Qualitative methods were used to assess capacity building outcomes. A sample of candidates from the 2006 and 2007 cohorts were selected for interview using stratified random sampling and supplemental purposive sampling. Twenty-five individual semi-structured interviews were conducted with candidates, their managers and mentors. Interviews were thematically analysed. The program components of teaching, mentoring and networking led to the development of research skills in candidates undertaking the program. This workforce development resulted in workplace change, particularly where the candidate’s project was ‘close to practice’ and they had management support. The leadership shown and partnerships developed by the program managers enhanced the workforce development and organisational change outcomes. Resources, such as backfill and incidentals, were useful for candidates, but practicalities, such as availability of replacement staff, limited effectiveness. This study showed the value of using a capacity building framework and demonstrated that undertaking research on a topic close to practice positioned candidates to drive change within their organisation.