The literature on the science‐policy interface suggests that stakeholders' perceptions of environmental planning and decision‐making processes can affect the uptake of conservation plans. Despite calls for more and better stakeholder engagement in conservation planning there is currently no empirical evidence on participants' perceptions of such processes. We asked participants of a conservation planning process and other key informants to evaluate their engagement experiences using normative governance principles (legitimacy, inclusiveness, fairness, accountability, integration, adaptability, transparency and capability). We analysed a large‐scale case‐study of species prioritization in Queensland, Australia. Conceptually, our systematic use of governance principles to interrogate perceptions of engagement showcased the utility of this analytical approach to uncover important issues influencing science‐policy uptake. Empirically, we showed that there remains considerable debate about how a normative conservation planning process should be. Our data revealed different interpretations of species prioritization, ranging from a deliberative process to define priorities in biodiversity conservation, to a technical, expert‐based process. Matters of ‘who’ was included affected stakeholders' perceptions of species prioritization. Perceived limitations of ‘how’ the process was conducted were also important, affected by the: (1) institutional culture of the Queensland Government; (2) lack of transparency; (3) limited flexibility to incorporate both emerging data and participants' suggestions in programme management; and (4) limited capability for implementation. These empirical data support existing evidence from studies in the broader field of collaborative planning. We draw from this literature to suggest how conservation planners can overcome the barriers to the uptake of prioritization priorities identified in or research. Copyright © 2016 John Wiley & Sons, Ltd and ERP Environment