There has been a resurgence of interest in agricultural input subsidy (AIS) programmes to boost agricultural productivity and food security. However there is considerable debate regarding the effectiveness and efficiency of AIS investments, including their impact on nutrition. The aim of this research was to examine the impact of Malawi’s AIS programme targeting mostly maize on overall food choices, by examining not just price and consumption of maize but crucially the effects of the AIS programme on consumption of other foods. It will also explore the wider context of food preferences and trade-offs, including by gender and socio-economic status.