Agriculture is facing up to an increasing number of challenges, including the need to ensure various ecosystem services and to resolve apparent conflicts between them. One of the ways forward for agriculture currently being debated is a set of principles grouped together under the umbrella term “ecological intensification”. In published studies, ecological intensification has generally been considered to be based essentially on the use of biological regulation to manage agroecosystems, at field, farm and landscape scales. We propose here five additional avenues that agronomic research could follow to strengthen the ecological intensification of current farming systems. We begin by assuming that progress in plant sciences over the last two decades provides new insight of potential use to agronomists. Potentially useful new developments in plant science include advances in the fields of energy conversion by plants, nitrogen use efficiency and defence mechanisms against pests. We then suggest that natural ecosystems may also provide sources of inspiration for cropping system design, in terms of their structure and function on the one hand, and farmers’ knowledge on the other. Natural ecosystems display a number of interesting properties that could be incorporated into agroecosystems. We discuss the value and limitations of attempting to ‘mimic’ their structure and function, while considering the differences in objectives and constraints between these two types of system. Farmers develop extensive knowledge of the systems they manage. We discuss ways in which this knowledge could be combined with, or fed into scientific knowledge and innovation, and the extent to which this is likely to be possible. The two remaining avenues concern methods. We suggest that agronomists make more use of meta-analysis and comparative system studies, these two types of methods being commonly used in other disciplines but barely used in agronomy. Meta-analysis would make it possible to quantify variations of cropping system performances in interaction with soil and climate conditions more accurately across environments and socio-economic contexts. Comparative analysis would help to identify the structural characteristics of cropping and farming systems underlying properties of interest. Such analysis can be performed with sets of performance indicators and methods borrowed from ecology for analyses of the structure and organisation of these systems. These five approaches should make it possible to deepen our knowledge of agroecosystems for actio