© 2017, Springer Science+Business Media B.V. and International Society for Plant Pathology. International organizations and national governments in resource-scarce settings regularly support programs for the control of animal diseases with the aim of improving smallholder food security. However, the impact of such disease control programs on smallholder food security remains unclear. Mixed methods designs that integrate the collection, analysis and interpretation of qualitative and quantitative data in a single study, are increasingly being used to achieve deeper explorations of complex topics. We propose a mixed methods design to assess the four pillars of food security and coping strategies among smallholders. The methodology is illustrated with a case study in the context of a transnational program for the control of Foot and Mouth Disease (FMD) in the Andean region, involving interviews with 632 smallholders in three countries. Quantitative data were analysed using multivariate analysis to describe smallholders’ profiles. Food Consumption Score (FCS) was calculated for each household. The qualitative phase involved developing themes to characterise these smallholders’ experiences using Thematic Analysis. Food acquisition capacity and coping strategies varied greatly across smallholders. Only nine (1.4%) of households had a FCS below the acceptable threshold, however, food stability was compromised across study areas. Household production, financial capacity, household demographics and food prices were the main factors influencing variation in food consumption. The case study presented here illustrates the use of a mixed methods approach to assess the four dimensions of food security and categorise key differences across smallholders during a single visit.