SummaryNatural resource management in Australia is beset with ‘wicked’ problems: diminishing biodiversity, increasing soil erosion, spreading soil salinity and global climate change all impact private landholders across rural Australia. These problems highlight the complexity of biodiversity conservation, and the need for inclusive, respectful approaches that enable the participation of rural communities, private landholders and government agencies to effectively manage biodiversity on public and private lands. To address these problems, some landholders, rural communities and other stakeholders are seeking evidence‐based solutions through directly applicable research. In this paper, we identify current barriers to such research and highlight principles and processes for co‐designing and managing research based on mutual trust, respect, power sharing and acceptance of various knowledge systems, as embodied in the theory of reconciliation ecology. We suggest that a ‘community of practice’ approach could assist in establishing effective deliberative relations as a basis for active collaboration in natural resource management research to address these complex problems.