Worldwide, agricultural production, food producers and retailers have a strong impact on biodiversity. Agriculture is the cause of up to 70% of the projected loss of biodiversity, mainly due to the expansion of cropland into forests, grasslands and savannahs. In the European agricultural landscape, intensive agriculture with its dependencies on the use of pesticides and synthetic fertilizers is another main cause of biodiversity loss. Therefore, the agricultural sector is asked to develop management options towards a more sustainable production and consumption pattern as set down in SDG 12 (Responsible Consumption and Production) and simultaneously to improve biodiversity indicators for SDG 15 (Life on Land). The Baseline Report of the EU Life-project ‘Biodiversity in standards and labels for the food sector’ analysed current certification standards and pointed out several gaps concerning the protection of biodiversity. In sum, effectively reducing the negative impacts of food production on biodiversity remains a big challenge due to the complexity of the matter. Although there exists a global agreement on the definition of ‘biodiversity’ (sensu UN Convention on Biological Diversity), the application of operable biodiversity indicators and procedures for monitoring trends of these indicators are still lacking behind. Finally, the allocation of responsibility within the supply chain with regard to the assessment and protection of biodiversity remains an open issue. We analyse the current practise of certification standards with regard to: (1) the definitions of biodiversity used; (2) the indicators used for documentation of compliance; and (3) the allocation of responsibilities within the supply chain.