Agroecological research has an important role in supporting evidence‐based land management to ensure food production is achieved whilst minimising the impacts on biodiversity and its associated ecosystem processes and services. This nexus between often competing priorities of optimal production and sustainability requires greater knowledge of management decisions to enact more sustainable and transformative practice change and to better conserve biodiversity. We highlight three key knowledge gaps in this area: (i) The use of appropriate indicators to measure dependencies and impacts on biodiversity; (ii) Methods to improve the management of resources to support the “health” of biodiversity within agroecosystems; (iii) Greater understanding of the ecosystem processes, and services generated and received across terrestrial and aquatic habitats. Synthesis and applications. Ecological research and robust science will play a vital role in supporting more sustainable food production. We see Journal of Applied Ecology playing a key role in promoting agricultural research that goes beyond a narrow focus on increasing output, and encourage more submissions at the interface of agriculture, ecology and biodiversity conservation, considering social and economic aspects for a sustainable future.