The critical importance of agricultural systems for food security and as a dominant global landcover requires management that considers the full dimensions of system functions at appropriate scales, i.e. multifunctionality. We propose that adaptive management is the most suitable management approach for such goals, given its ability to reduce uncertainty over time and support multiple objectives within a system, for multiple actors. As such, adaptive management may be the most appropriate method for sustainably intensifying production whilst increasing the quantity and quality of ecosystem services. However, the current assessment of performance of agricultural systems doesn’t reward ecosystem service provision. Therefore, we present an overview of the ecosystem functions agricultural systems should and could provide, coupled with a revised definition for assessing the performance of agricultural systems from a multifunctional perspective that, when all satisfied, would create adaptive agricultural systems that can increase production whilst ensuring food security and the quantity and quality of ecosystem services. The outcome of this high level of performance is the capacity to respond to multiple shocks without collapse, equity and triple bottom line sustainability. Through the assessment of case studies, we find that alternatives to industrialized agricultural systems incorporate more functional goals, but that there are mixed findings as to whether these goals translate into positive measurable outcomes. We suggest that an adaptive management perspective would support the implementation of a systematic analysis of the social, ecological and economic trade-offs occurring within such systems, particularly between ecosystem services and functions, in order to provide suitable and comparable assessments. We also identify indicators to monitor performance at multiple scales in agricultural systems which can be used within an adaptive management framework to increase resilience at multiple scales.