ABSTRACT The Western Highlands of Guatemala are dominated by small-scale farming in indigenous communities. Mountain conditions and overpopulation have led to expansion of the agricultural frontier with consequent degradation, decreasing yields, poverty and malnutrition. Several non-government organizations (NGO) have carried out interventions to rescue the milpa system and diversify farming systems. We used the Framework for the Evaluation of Management Systems using Indicators (MESMIS) to evaluate farm sustainability after such interventions. We analysed data from four participating NGOs, interviewing 50 farmers with several years of collaboration as alternative systems, and 50 farmers of recent incorporation as reference systems. A trend towards moderate improvements was found in yields, food availability and reduced losses due to pests, diseases and climatic events. Given the environmental conditions and farm size it seems unlikely that most farms could achieve food self-sufficiency. In some cases, the increase in yields and food security correlate with a higher external input dependence. Even with agroecological interventions, external inputs might be needed. Direct indicators need to be measured in future studies for soil quality and erosion control. Even though the study cases showed regional differences, it was possible to develop a common, robust group of indicators, along with some case-specific ones.