An experiment has been designed in the Highlands of Madagascar with the aim to produce multi-criteria indicators of performance of agroecological practices. In this experiment, different traditional and innovative practices were tested in field conditions with the assumption that practices that enhance soil biodiversity and soil ecological processes are the one that best promote plant production, yield and sustainability. Both ecological and agronomic performances were confronted with socio-economic performance defined by farmers in order to propose innovative practices adoptable by farmers. A 2-year field experiment with 16 different practices, replicated 4 times, was designed in the Highlands of Madagascar with upland rice as the main crop. Many soil and plant parameters were measured: 73 parameters to describe soil biodiversity and soil ecological processes, 19 descriptors to measure rice production, nutrition and yield, and 8 socio-economic descriptors. This study led to the production of a useful indicator allowing to evaluate an agroecological practice on the way it promotes soil health and especially soil biodiversity, crop yield and socio-economical requirements which are the main limits for practice adoption. We measured interesting relations between soil ecological descriptors and agronomic descriptors.