Our paper ‘Loading the dice in favour of the farmer: reducing the risk of adopting agronomic innovations’ revealed mean increases but also large variation in the impact of four agroforestry practises on maize yield, as experienced by farmers in Malawi. This prompted a response from Sileshi and Akinnifesi that was critical of the data and methods used. Their main concern was that farmers did not necessarily manage crops identically in plots with and those without trees, so the yield differences that we measured may be partly caused by these differences in crop management. We argue here that it is valid and useful to look at the actual effect on crop yield of farmers having trees intercropped with maize, rather than controlling for how the crop is managed, because this is what happens in the real world. Farmers respond to having trees in their field by treating their crop differently, so this is part of the system response to having trees in fields. Attempts to eliminate this will result in measuring an artefact rather than the real impact of trees on crop yield. By doing this, we revealed important variation in the impact of trees on crop yield amongst farmers, and we argue that it is important to explore, assess and communicate to farmers and development actors the extent and implications of this variation. Understanding the contextual factors that determine who is likely to benefit most from an innovation and for whom it is less suitable can then be incorporated in scaling up, so that targeting of innovations and the appropriateness of messages given to farmers are continuously refined.