Inspired by Liberation Theology, which swept through the Catholic Church in Latin America after the 1960s, Ruiz's diocese helped some hundreds of thousands of indigenous Maya people in Chiapas who were among Mexico's poorest marginalized communities.

Vatican II encouraged that sermons be translated and read to communities in their local languages and that the Church be more involved in addressing social problems,[8] such as those occurring in Central and South America.

[9] For Ruiz, his participation in the Second Vatican Council allowed time for reflection on the decisions and actions carried out under his administration, which brought him a long way from the somewhat naïve enthusiasm which he'd had during his first years as bishop.

This was a position which he held until 1972 when elections for secretary general chose Archbishop Alfonso López Trujillo, who proceeded to replace progressive department heads, such as Ruiz, with his own conservative allies.

[2]: 25  Out of this conference, held in Medellín, Colombia, in 1968, emerged a consensus that the root of poverty and oppression in Latin America was a systemic problem, one which grew out of the ethic of expansion and development by United States imperialism.

The diocese of San Cristóbal de las Casas (Chiapas), under Samuel Ruiz's direction, began to redefine evangelization methods and to abandon the traditional approach of Europeanizing indigenous peoples, instead incarnating the gospel in the local culture of each community.

[4]: 114  By doing so, and by translating the Bible into indigenous languages, this work allowed for the poor of San Cristóbal to begin identifying parallels between their own experiences of oppression with those in Biblical passages, most notably the Exodus.

[6]: 72  Indigenous poor no longer accepted the "low wages they earned on plantations, the lack of security in their land titles, the corruption of government agencies, and the abuses of merchants and landowners", instead using "their religious faith and interpretation of the Bible to create concrete solutions to immediate problems".

[9] In 1989, Bishop Ruiz founded the Fray Bartolomé de Las Casas Rights Center to push back against increasing violence against indigenous and campesino activists in his diocese.

[12] This theology of liberation, however, appeared threatening to government structures and those with political and economic power, and in some cases oppression of rural and urban poor in Mexico and other areas of Latin America grew worse.

Areas which practiced these new ways of interpreting the Bible and encouraged the poor to fight for their human rights were labeled Marxists and, often under government orders, para-militaries conducted counter-insurgent campaigns using low-intensity warfare to target civilians who supported these resistance movements.

On 1 January 1994, the date that NAFTA came into effect, a group of several hundred indigenous guerrillas occupied several transit routes and government offices in San Cristóbal de las Casas and other cities in the highlands.

[4] The Mexican government, who for years had silenced protests in Chiapas in order to create the political and economic conditions needed to ensure its admission into NAFTA, was outraged and blamed Ruiz's pastoral practices and consciousness-raising techniques as one of the roots of the Zapatista Uprising.

[13] The PRI, which had monopolized power for nearly 70 years, attempted to respond to the uprisings with military pressure – implementing strategies of low-intensity warfare to terrorize the civilian population that supported the Zapatistas.

[16] The PGR repressive acts got to the extreme of arresting the San Cristóbal de Las Casas, Chiapas, Catholic Bishop, Samuel Ruiz García, for aiding to conceal the Zapatistas guerrilla activity.

[19] hurt by the 24 May 1993, political assassination of a Prince of the Catholic Church, the Guadalajara, Mexico Cardinal Juan Jesús Posadas Ocampo, that precisely that Agency, the PGR, had left it unresolved.

On 9 February 1995, in a televised special Presidential broadcast, President Ernesto Zedillo announced Subcomandante Marcos to be one Rafael Sebastián Guillén Vicente, born 19 June 1957, in Tampico, Tamaulipas, to Spanish immigrants, a former professor at Universidad Autónoma Metropolitana School of Sciences and Arts for the Design.

This committed the parties to basic respect for the diversity of the indigenous population of Chiapas, granted the right to participation in determining their development plans, control over administrative and judicial affairs, and self-government.

[29] On 24 January 2011, at the age of 86, Samuel Ruiz García died at Hospital Ángeles del Pedregal in Mexico City, due to respiratory failure and other complications, including high blood pressure and diabetes.

In 1996, Samuel Ruiz received the Pacem in Terris Peace and Freedom Award for his fight against injustice and institutionalized violence inflicted on the poor and oppressed of his diocese of San Cristóbal de las Casas.