Introduction: The optimal approach to engage the public in healthcare decision-making is unclear. Approaches range from deliberative citizens' juries to large population surveys using discrete choice experiments. This study promotes public engagement and quantifies preferences in two key areas of relevance to the industry partners to identify which approach is most informative for informing healthcare policy. Methods and analysis: The key areas identified are optimising appropriate use of emergency care and prioritising patients for bariatric surgery. Three citizens' juries will be undertaken - two in Queensland to address each key issue and one in Adelaide to repeat the bariatric surgery deliberations with a different sample. Jurors will be given a choice experiment before the jury, immediately following the jury and at approximately 1 month following the jury. Control groups for each jury will be given the choice experiment at the same time points to test for convergence. Samples of healthcare decision-makers will be given the choice experiment as will two large samples of the population. Jury and control group participants will be recruited from the Queensland electoral roll and newspaper advertisements in Adelaide. Population samples will be recruited from a large research panel. Jury processes will be analysed qualitatively and choice experiments will be analysed using multinomial logit models and its more generalised forms. Comparisons between preferences across jurors predeliberation and postdeliberation, control participants, healthcare decision-makers and the general public will be undertaken for each key issue. Ethics and dissemination: The study is approved by Griffith University Human Research Ethics Committee (MED/10/12/HREC). Findings of the juries and the choice experiments will be reported at a workshop of stakeholders to be held in 2015, in reports and in peer reviewed journals.