The global challenge of feeding two billion more people by 2050, using more sustainable agricultural practices whilst dealing with uncertainties associated with environmental change, requires a transformation of food systems. We present a new perspective for how advances in network science can provide novel ways to better understand, harness, and restore multiple ecological processes in agricultural environments. We describe: (i) a network-focused framework for managing agro-ecosystems that accounts for the multiple interactions between biodiversity and associated ecosystem services; (ii) guidance for incorporating socio-economic factors into ecological networks; and (iii) the potential to upscale network methods to inform efforts to build resilience, including global food-supply chains. In doing so we aim to facilitate the application of network science as a systems-based way to tackle the challenges of securing an equitable distribution of food.