Despite growing recognition of the pressing need for companies to protect biodiversity, research has not yet provided a comprehensive overview to help guide companies on effective biodiversity management. This study identifies a package of intra-organisational biodiversity management controls that may be effective across multiple organisational contexts as well as individual controls that companies can choose from according to their specific contexts. For this purpose, we undertook an exploratory multiple case-study, selecting critical cases from the food sector on the basis of this industry’s enormous impacts on biodiversity loss and its existential dependence on preserving biodiversity. In analysing our interview and archival data we applied a framework of management control categories to investigate the research question ‘How do food companies use management control systems to address biodiversity?’ Our study contributes to practice and theory by providing a systematic overview of management controls and practices targeting key issues of biodiversity loss. Whilst confirming there is no one-size-fits-all approach, our findings indicate that companies should strive to integrate biodiversity-related controls with their core business, interlink biodiversity controls with existing sustainability controls, and complement informal with formal controls.