In between 1973 and 1976, he was Rector of Externado San José, which was precisely a moment when the school was going through a deep identity crisis.
The consequences of the Second Vatican Council and the Episcopal Conference of Medellín had made Externado San José express a preference for the poor and to prioritize education that contributed to modify the social differences in El Salvador.
This sort of discourse was not well received by the Salvadoran elites, who had been traditionally served by Externado San José.
He was not singled out in propagandistic government pamphlets against critical intellectuals until towards the end of his life, when his name started figuring in the lists of Jesuits who were accused of being revolutionaries.
To prepare himself for academia, he travelled to Spain, and in 1978 he completed a PhD in Social Anthropology in Universidad Complutense in Madrid.
He visited Washington, D.C., on repeated occasions, to testify in the corresponding committees in the United States Congress, to defend the rights of Salvadoran refugees.
[1] Segundo Montes did research and wrote on social stratification, land ownership, the possibilities for democracy and the military.
His work on these issues is still a dominant influence on the theoretical frameworks employed by researchers to analyse Salvadoran society.
His published articles included an analysis of economic, political, and other motives for Salvadoran emigration to the United States.
It addressed claims by the United States government that Salvadoran immigrants were economic refugees who therefore did not qualify for political asylum.
Their murders marked a turning point in the Salvadoran civil war (see History of El Salvador).