Manuel Gómez, 61, is walking along the San Cristóbal de las Casas ring road in southern Mexico, wearing a long white robe and a purple chechia hat. "I was born a Catholic, became a Presbyterian and now I'm a Muslim," this Tzotzil Indian explains. Since converting to Islam in 1995 he has gone by the name of Muhammad. Tens of thousands of residents of this town in Chiapas state, home to the Zapatista Army of National Liberation (EZLN), have turned their backs on Catholicism.

There are not many Muslims, but Protestants and evangelicals now account for more than a quarter of the state's population of 4.8 million. The mass conversions, which have coincided with the violent expulsion of large numbers of peasants from claimed land, worry the Catholic clergy, who welcomed Pope Benedict XVI last month in Guanajuato state.

Muhammad prays five times a day in his decrepit house. "I've had two invitations to go to Mecca," says this fruit and vegetable vendor, who had never set foot outside Chiapas before becoming a Muslim. His wife Nura, formerly Joana, wears an Islamic headscarf but has retained the traditional Tzotzil goat-hair dress. "There's no question of us giving up the culture of our ancestors," Muhammad adds.

Not far from there, at the end of a dusty alley, a renovated building houses an Islamic school run by the Morabitum movement, part of the Sufi branch of Islam. "About 20 children are learning the Qur'an phonetically," says imam Hajj Idriss, aka Estebán López, who leads the Friday prayer meeting. This 60-ish Spaniard arrived in Chiapas in 1995 to establish Islam in Mexico and since then some 500 Indians have converted here.

There are dozens of Evangelical churches in the town (population 190,000). Most branches of Protestantism are represented, with Methodists, Baptists, Adventists and so on. "In the 1930s the first missionaries translated the Scriptures into various Indian languages," says Aída Hernández, a specialist on religions at the Social Anthropology Research Centre (Ciesas). "Chiapas is now home to Mexico's largest Protestant community." Their share of the total population – 27% – has almost doubled in 20 years, according to the Mexican Statistics Institute.

On Sunday morning, in another poor suburb to the north, the Sólo Cristo Salva Pentecostal church is packed. Manuel Días, a 20-ish Tzotzil, is pumping out joyful hallelujahs on the electronic organ. The faithful wave their arms, clap their hands and dance with eyes closed to the sound of rock, pop or salsa.

"The Indians are disappointed by Catholicism, which bears the mark of colonial rule and authoritarian mestizo priests. The evangelical churches, which respect their parallel beliefs, are better suited to their spiritual needs and demands for solidarity in the face of poverty, illiteracy and discrimination," says Gaspar Marquecho, an anthropologist at the Autonomous University of Chiapas.

Vincente García, 33, a Pentecostalist street vendor, "gave up drink thanks to God". But he paid a high price for his conversion. "The Catholics drove out my family," says the former peasant-farmer, who was forced to leave San Juan Chamula. From the 1960s to the late 1990s this Tzotzil town, some 10km north of San Cristóbal, was the scene of violent religious strife. The unrest has since spread all over the area. "It was get out or die," says Pascuala López, an Indian of 25, whose house in the village of Huixtán, south-west of the city, was burned down. "Crimes are less frequent now but the tension persists," Marquecho says. Last June a pastor in Huixtán, home to the Tzeltal Indians, was murdered with his wife and 14-year-old son.

From the end of the 1960s, Samuel Ruiz, bishop of San Cristóbal, opposed such violence. An advocate of liberation theology, he established close links with Subcomandante Marcos, who in 1994 launched the Zapatista uprising in San Cristóbal in defence of Indian rights. When the bishop died in January 2011 the EZLN paid tribute to him. "But Marcos did not want to get involved in religious conflicts and encouraged the evangelicals to stand up for themselves," Marquecho adds. "Their mobilisation, sometimes in arms, explains the drop in the number of people being displaced."

"The conflicts between communities are not about religion, but about politics and the economy," says Sandra Canas, an anthropologist at the University of Texas at Austin. "By becoming evangelicals the Indians break with a corrupt, authoritarian system run by local notables, whose dominant position is rooted in Catholicism. Landowners throw the Indians out to stop them challenging their authority."

Appointed bishop of San Cristóbal de las Casas in 2000, Felipe Arizmendi condemns such acts and favours cultural diversity, but he is determined to win back lost ground by increasing the number of priests covering the state, up from 66 to 90 in 12 years. "Our 60 seminarists are all learning a native language," he adds, "and the pope's visit will boost this drive."

This article originally appeared in Le Monde