Public health interventions that involve strategies to re-localise food fail in part because they pay insufficient attention to the global history of industrial food and agriculture. In this paper we use the method of comparative ethnography and the concept of structural violence to illustrate how historical and geographical patterns related to colonialism and industrialisation (e.g. agrarian change, power relations and trade dependencies) hinder efforts to address diet-related non-communicable diseases on two small islands. We find comparative ethnography provides a useful framework for cross-country analysis of public health programmes that can complement quantitative analysis. At the same time, the concept of structural violence enables us to make sense of qualitative material and link the failure of such programmes to wider historical and geographical processes. We use ethnographic research carried out from April to August 2013 and from June to July 2014 in Trinidad (with follow-up online interviews in 2018) and in Nauru from February to May 2010 and August 2010 to February 2011. Our island case studies share commonalities that point to similar experiences of colonialism and industrialisation and comparable health-related challenges faced in everyday life.