BACKGROUND: Workplace health interventions incorporating qualitative and quantitative components (mixed methods) within a Participatory Action Research approach can increase understanding of contextual issues ensuring realistic interventions which influence health behaviour. Mixed methods research teams, however, face a variety of challenges at the methodological and expertise levels when designing actions and interventions. Addressing these challenges can improve the team's functionality and lead to higher quality health outcomes. In this paper we reflect on the data collection, implementation and data analysis phases of a mixed methods workplace health promotion project and discuss the challenges which arose within our multidisciplinary team. METHODS: This project used mixed methods within a Participatory Action Research approach to address workers' sun safety behaviours in 14 outdoor workplaces in Queensland, Australia, and elucidate why certain measures succeeded (or failed) at the worker and management level. The project integrated qualitative methods such as policy analysis and interviews, with a range of quantitative methods - including worker surveys, ultraviolet radiation (UVR) exposure measurement, and implementation cost analyses. RESULTS: The research team found the integration of qualitative and quantitative analyses within the Participatory Action Research process to be challenging and a cause of tensions. This had a negative impact on the data analysis process and reporting of results, and the complexity of qualitative analysis was not truly understood by the quantitative team. Once all researchers recognised qualitative and quantitative data would be equally beneficial to the Participatory Action Research process, methodological bias was overcome to a degree to which the team could work cooperatively. CONCLUSIONS: Mixed methods within a Participatory Action Research approach may allow a research team to discuss, reflect and learn from each other, resulting in broadened perspectives beyond the scope of any single research methodology. However, cohesive and supportive teams take constant work and adjustment under this approach, as knowledge and understanding is gained and shared. It is important researchers are cognisant of, and learn from, potential tensions within research teams due to juxtaposed philosophies, methodologies and experiences, if the team is to function efficiently and positive outcomes are to be achieved.