Effective conservation requires knowledge exchange among scientists and decision-makers to enable learning and support evidence-based decision-making. Efforts to improve knowledge exchange have been hindered by a paucity of empirically-grounded guidance to help scientists and practitioners design and implement research programs that actively facilitate knowledge exchange. To address this, we evaluated the Ningaloo Research Program (NRP), which was designed to generate new scientific knowledge to support evidence-based decisions about the management of the Ningaloo Marine Park in north-western Australia. Specifically, we evaluated (1) outcomes of the NRP, including the extent to which new knowledge informed management decisions; (2) the barriers that prevented knowledge exchange among scientists and managers; (3) the key requirements for improving knowledge exchange processes in the future; and (4) the core capacities that are required to support knowledge exchange processes. While the NRP generated expansive and multidisciplinary science outputs directly relevant to the management of the Ningaloo Marine Park, decision-makers are largely unaware of this knowledge and little has been integrated into decision-making processes. A range of barriers prevented efficient and effective knowledge exchange among scientists and decision-makers including cultural differences among the groups, institutional barriers within decision-making agencies, scientific outputs that were not translated for decision-makers and poor alignment between research design and actual knowledge needs. We identify a set of principles to be implemented routinely as part of any applied research program, including; (i) stakeholder mapping prior to the commencement of research programs to identify all stakeholders, (ii) research questions to be co-developed with stakeholders, (iii) implementation of participatory research approaches, (iv) use of a knowledge broker, and (v) tailored knowledge management systems. Finally, we articulate the individual, institutional and financial capacities that must be developed to underpin successful knowledge exchange strategies. •Integration of science into decision-making processes is a significant challenge.•Knowledge exchange underpins learning and evidence-based decision-making.•We provide empirically grounded guidance for improving knowledge exchange.•The capacities required to support knowledge exchange processes are also identified.