The context of family farming in Madagascar's highlands calls for tailored criteria to inform farmers and decision-makers about the strengths and limitations of agroecological practices. Here we suggest a set of 11 indicators considered relevant for assessing the sustainability of these cropping systems, essentially focused on subsistence. These indicators aim to assess the relevance of cropping systems in terms of food production, maintenance of soil fertility, connection with livestock systems, profitability, and labor productivity. They were selected to evaluate sustainability aspects at the field level, while also addressing issues from a systemic perspective: at farm (fodder availability, labor) and territory levels (biomass use). We have applied these indicators to two contrasting systems: rice monocropping and rotation of rice-fish farming and potato, with different fertilization methods. Farming systems sustainability can hardly be assessed based on field scale evaluation, as there are many trade-offs and synergies between sustainability components emerging at farm scale. Based on this diagnosis of cropping systems, a farm model will be mobilized to evaluate the feasibility of these cropping systems at farm scale, i.e. taking into account resource availability at the household level. In addition to this contextualization of cropping systems, the modeling process will allow exploring different scenarios of agroecological innovation at farm scale.