In 1994, the Zapatistas took up arms claiming for indigenous people rights in Chiapas, Mexico. After 12 days of civil war, the government called for dialogue. Nevertheless, since then, it has deployed a “low intensity war” over the Zapatistas. At the same time, the Zapatistas started to implement a new set of institutions, which have allegedly enhanced their socio-economic situation. The purpose of this study is to elucidate this ambiguous theoretical effect on the wellbeing of the communities under harassment. This paper generates a unique dataset, linking socio-economic variables from the Mexican Census with different measures of conflict intensity at the locality level, based on geo-coded influence areas. The present investigation controls for the endogeneity in the relationship between conflict and the socio- economic performance, instrumenting the former by the distance from each locality to a strategic military spot defined by the Zapatista Army. The results imply that the impact of the Zapatista institutions has surpassed the negative effect of the civil strive, suggesting that: i) bottom-up policies carried out by grass-root organizations, even in times of conflict, might represent an appropriate path for development; and ii) the Mexican government should recognize the Zapatista autonomy and its right for self-determination.