In this article we consider the role that contextual factors play in science innovation systems - that is, the choice architecture, that influences the orientation and outcomes of publicly-funded research. More specifically, we examine how choice architects, particularly policymakers and funding administrators, can affect the decision-making behaviour of researchers. The context for today’s science innovation systems continues to shift as governments seek solutions to the world’s “grand societal challenges” such as climate change and ageing populations, in addition to greater and more demonstrable impact from funded research. This means that the assumptions of “basic research [being] performed without thought of practical ends” (Bush, 1945) that have shaped such projects, actually run counter to the growing expectations of greater commercialisation and use of multidisciplinary mission-led approaches. We argue that a closer examination of the choice architecture of publicly-funded research is required to understand and address how these potentially conflicting objectives may be pursued most productively through interventions that could form the basis of a novel, behaviourally-based toolkit for science innovation policy.