Studies on the effects of research and innovation in agriculture have been largely characterised by efforts to make a connection between expenditure and productivity. A number of issues have challenged the ability of productivity to measure the effects of research, namely, in recent years, increasing efforts towards improving the environmental performance of the farming sector. Besides environmental concerns, however, a number of recent concepts have emerged that are shaping the current research and policy agenda and which could result in a revision of the productivity concepts used to evaluate research impacts. The objective of this paper is to discuss these issues and their implications for studies on the impact of research and innovation. We address, in particular, the following issues: a) the development of the of bioeconomy and related concepts such as the circular economy, resource efficiency and bio-refinery; b) the connection with entrepreneurship and eco-innovation; c) changing tools in research assessment, in particular the widespread use of Life Cycle Assessment (LCA); and d) the evolving concepts of sustainability and ecosystem services. We argue that while the traditional notion of productivity, intended as output/input ratio, maintains (and may be strengthens) its role on the aggregate, a more analytical interpretation of the pathways towards research impacts is needed, as well as a broadened view of productivity and its determinants.