Background Evidence-based practice aims to achieve better health outcomes in the community. It relies on high quality research to inform policy and practice; however research in primary health care continues to lag behind that of other medical professions. The literature suggests that research capacity building (RCB) functions across four levels; individual, team, organisation and external environment. Many RCB interventions are aimed at an individual or team level, yet evidence indicates that many barriers to RCB occur at an organisational or external environment level. This study asks senior managers from a large healthcare organisation to identify the barriers and enablers to RCB. The paper then describes strategies for building allied health (AH) research capacity at an organisational level from a senior managers' perspective. Methods This qualitative study is part of a larger collaborative RCB project. Semi-structured in-depth interviews were conducted with nine allied health senior managers. Recorded interviews were transcribed and NVivo was used to analyse findings and emergent themes were defined. Results The dominant themes indicate that the organisation plays an integral role in building AH research capacity and is the critical link in creating synergy across the four levels of RCB. The organisation can achieve this by incorporating research into its core business with a whole of organisation approach including its mission, vision and strategic planning. Critical success factors include: developing a co-ordinated and multidisciplinary approach to attain critical mass of research-active AH and enhance learning and development; support from senior managers demonstrated through structures, processes and systems designed to facilitate research; forming partnerships to increase collaboration and sharing of resources and knowledge; and establishing in internal framework to promote recognition for research and career path opportunities. Conclusions This study identifies four key themes: whole of organisation approach; structures, processes and systems; partnerships and collaboration; and dedicated research centres, units and positions. These themes form the foundation of a model which can be applied to assist in achieving synergy across the four levels of RCB, overcome barriers and create an environment that supports and facilitates research development in AH.