There is increasing recognition in academic circles of the importance of adaptive governance for the sustainability of social-ecological systems, but little examination of specific implications for the 34% of land-use where human activities are pervasive but potentially commensurate with functioning ecosystems: agricultural production systems. In this paper, we argue for the need to view food systems and agro-ecosystems as multi-scalar complex adaptive systems and identify five key challenging characteristics of such systems: multi-causality; cumulative impacts; regime shifts; teleconnections and mismatch of scales. These characteristics are necessary features of multi-scalar adaptive systems, and apply equally to social and natural subsystems. We discuss the implications of these characteristics for agricultural production systems and consider how governance can rise to these challenges. We present five case studies that highlight these issues: pollinator declines; payments for ecosystem services; pest control and pesticide resistance; downstream aquatic systems in Tasman Bay, New Zealand; and riparian buffers in Puget Sound, USA. From these case studies we derive recommendations for managing agricultural systems, both specific and general. Ultimately, adaptive governance of agro-ecosystems will likely hinge upon three paradigm shifts: viewing farmers and ranchers not only as food producers but also as land and water managers; seeking not yield maximization but rather resilient management of food ecosystems; and critically, as it transcends the production-system literature, engaging broad audiences not only as consumers but also citizens.