For many years, biodiversity has been in drastic global decline, faster than at any time in human history. The impact of economic activities on biodiversity is widely recognised and companies bear a great responsibility for the conservation, sustainable use, and restoration of biodiversity. Biodiversity accounting serves as an important tool for companies to operationalise their engagement with biodiversity. However, biodiversity is inherently complex and companies’ understanding is often limited by a lack of knowledge. We argue that accounting systems are constructed through social processes, so are biodiversity knowledge and values. Recognising that individuals’ biodiversity knowledge and assignment of value and significance to biodiversity differs depending on their social and cultural context, underscores the necessity to include diverse stakeholder voices in biodiversity accounting. We adopt this multi-stakeholder approach to design a biodiversity accounting process and scheme for the sewage industry, through co-creation of knowledge in form of a stakeholder dialogue. By adopting this multi-stakeholder approach, we hope to significantly enhance biodiversity accounting by addressing its complex, multi-stakeholder nature, and integrating diverse perspectives on valuing and measuring biodiversity.