"The next bombs will be in your cassock", read pamphlets found outside one of the churches. During the Pope's visit, protests are expected on issues ranging from indigenous rights to an ongoing sexual abuse scandal in the Church.
Francis, who hails from Argentina and is the first Latin American pope, will arrive in Chile on Monday. He will celebrate Mass for the Mapuche in southern Araucania province on Wednesday and meet with representatives from other indigenous groups at a private lunch. A small minority of Mapuches have used violence to further their cause, and in recent years churches have been targeted.
In a sense, every papal liturgy in St. Peter's Basilica has symbolic value, but rarely was that symbolism more overtly on display than on Sunday, when Pope Francis led a Mass for the Catholic Church's January 14 World Day of Migrants and Refugees.
Earlier in August, Francis released a message for the World Day of Migrants and Refugees, in which he recalled that this been a priority for him from the beginning of his papacy, expressed in his first trip outside Rome to the Italian island of Lampedusa in July 2013.
Most of the newcomers are Haitians.
Sebastian Pinera, Chile's president-elect, condemned the attacks in a statement on Twitter.
On his visit to Peru, the second leg of the January 15-22 tour, Francis will also find a destabilizing political corruption crisis has reopened wounds from one of the country's darkest periods of human rights abuses. The El Nino storms killed more than 100 people and destroyed bridges, infrastructure and homes in hundreds of villages in an already poor area.
The pope's message, which was released on November 24 previous year and delivered on January 1, urged countries to view global migration "with confidence as an opportunity to build peace" instead of seeing it as a threat.
Chile's Catholic churches have been struggling to improve their image after a sex scandal involving Rev. Fernando Karadima.
The Vatican in 2011 sentenced Karadima to a lifetime of "penance and prayer" after confirming what his victims had been saying for years but what Chile's Catholic leadership refused to believe: that Karadima had sexually abused them. That plan went awry and Barros was appointed to Osorno.
But if he utters the word "corruption" in Peru, it will have particular significance.
A giant Christ statue in Peru's capital city has been damaged by fire days before Pope Francis is set to arrive in the South American nation.
The former CEO of Odebrecht has admitted that company executives paid bribes and campaign contributions to secure public works contracts around the continent. Many Peruvians believe the pardon was done to secure support during the impeachment vote from a political party led by Fujimori's son. The Synod on the Amazon will bring bishops and cardinals from around the world to the Vatican to discuss how to best help the Amazonian people.