Advances in sequencing technologies and declining costs are increasing the accessibility of large-scale biodiversity genomic data sets. To maximise the impact of these data, a careful, considered approach to data management is essential. However, challenges associated with the management of such data sets remain, exacerbated by uncertainty among the research community as to what constitutes best practices. As an interdisciplinary team with diverse data management experience, we recognise the growing need for guidance on comprehensive data management practices that minimise the risks of data loss, maximise efficiency for stand-alone projects, enhance opportunities for data reuse, facilitate Indigenous data sovereignty and uphold the FAIR and CARE Guiding Principles. Here, we describe four personas reflecting user experiences with data management to identify data management challenges across the biodiversity genomics research ecosystem. We then use these personas to demonstrate realistic considerations, compromises, and actions for biodiversity genomic data management. We also launch the Biodiversity Genomics Data Management Hub (https://genomicsaotearoa.github.io/data-management-resources/), containing tips, tricks and resources to support biodiversity genomics researchers, especially those new to data management, in adopting best practice. We aim to support the biodiversity genomics community in embedding data management throughout the research life cycle to maximise research impacts and outcomes.