Ensuring food security and halting biodiversity decline are urgent, interconnected challenges. Drawing on the natural and social sciences, I propose an interdisciplinary research agenda to address these challenges. My goal is to develop a global theory that explains which properties of social-ecological systems benefit both biodiversity conservation and food security (and which benefit one but not the other). This holistic, systems-oriented approach radically differs from existing work: The most high-profile framing at present focuses on the question how to increase agricultural yields without compromising biodiversity. By contrast, a systems-oriented approach recognizes yield as just one variable alongside others that also influence biodiversity and food security. I will use a multi-scale approach that balances the likely trade-offs between depth and generality. Using a specifically developed typology of social-ecological system properties, I will investigate rural landscapes as social-ecological systems at three levels of detail. First, drawing on expert knowledge, I will develop a global database of at least 50 relevant systems, relating general system properties to indicators of food security and biodiversity. Second, I will conduct in-depth workshops on 15-20 social-ecological systems worldwide to reveal in more detail the causal linkages between system properties, food security and biodiversity. Third, I will conduct an in-depth empirical case study on food security and biodiversity in Ethiopia. This will complement the other components by highlighting the nature of potentially important regional subtleties. My multi-scale approach effectively combines high ambition and high feasibility. SESyP will produce new tools and a holistic theory of relevance to researchers, policy makers, supra-national bodies and non-governmental organizations worldwide.