ROME, Italy — When Sicilian Mafia superboss Bernardo Provenzano was nabbed in a little farmhouse near Corleone, Sicily, in April 2006 after 43 years on the lam, police found one of his five Bibles especially interesting. Among the worn Catholic prayer cards and tattered photos of Jesus Christ stuffed between the pages, Provenzano had written a secret code, including dots, arrows and other notations he used to guide the Cosa Nostra from his secret hideout to kill, threaten, extort and rob.

Provenzano, a devout Catholic who reportedly watched Mass on television or listened to it on the radio every day, had also underlined and retyped scores of passages from both the Old and New Testament, including several from the Book of Revelation, including one (17:7) that implied he was doing God's work: "For God hath put in their hearts to fulfill his will, and to agree, and give their kingdom unto the beast, until the words of God shall be fulfilled."

Provenzano was hardly the first Mafioso to hide behind his Catholic faith. There has always been a close connection between the Catholic Church and mafia-style organized crime syndicates, especially in the small villages of southern Italy where local priests often are complicit in criminal activity, either by doling out sacred forgiveness for heinous crimes or acting as character witnesses for the most unworthy criminals.

Mobster hideouts often are plastered with Catholic icons, including rosaries, crucifixes and statues of the Virgin Mary. But on Saturday, when Pope Francis visited the epicenter of the ‘Ndrangheta criminal gangland in Calabria, he made it clear that organized crime had to end, calling the ‘Ndrangheta’s activity an “adoration of evil and contempt for the common good.”

Deviating from his prepared script, Francis repeated his previous condemnation of criminal activity, telling a crowd of 200,000 faithful that those who are involved in mafia-style organized crime gangs should consider themselves excommunicated immediately (though the papal spokesman was quick to clarify that excommunication is a legal act and the pope’s words did not reflect a change in Canon law on the matter).

"Those who in their lives follow this path of evil, as mafiosi do, are not in communion with God. They are excommunicated,” said the Pope. “This evil must be fought against. It must be pushed aside. We must say no to it.”

Francis’s message was not just meant for the gangsters. John Dickie, professor of Italian studies at University College London and author of several books on Italian organized crime including the recent Mafia Republic, told The Daily Beast that the pope was talking to the priests, too.

“The real audience of Pope Francis’s message was the local church,” Dickie told The Daily Beast. “There is a very long history of silence and complicity with the Catholic Church and the Mafia. For years many priests have been happy to allow the Mafia to dress themselves up as upstanding members of communities.”

Now, Dickie says, the church is distancing itself from the perceived alliance. The move started with John Paul II, who was the first pope to ever use the word “mafia” when he denounced the Sicilian Cosa Nostra at a Mass in Agrigento in 1993. Before that, the Church had largely turned a blind eye to the criminal gangs, even denying in some cases that the Mafia existed at all.

John Paul II’s words had two significant impacts. A handful of Mafiosi serving sentences in Italian prisons started cooperating with the police, becoming “pentiti” or turncoats. But the Mafia also took its revenge, setting off bombs in Rome, Florence and Milan that killed ten people. The attacks targeted cultural entities like the Uffizi in Florence, and also hit the basilica of San Giovanni in Rome—John Paul II’s titular church.

So far, there has been no retaliation or direct threat against Francis, who continues to defy his security detail by refusing to use the bullet-proof popemobile in crowds. But in November 2013, Nicola Gratteri, a leading anti-mafia prosecutor in Calabria admitted that Pope Francis was making criminals “very nervous,” warning that the pope’s hard line against organized crime could put him in danger.

In an interview with Il Fatto Quotidiano newspaper, Gratteri, who lives under constant police protection for his own anti-Mafia work, said the pope should be cautious. “If the godfathers can find a way to stop him, they will seriously consider it,” Gratteri said. “Those who have up until now profited from the influence and wealth drawn from the church are getting very nervous. For many years, the mafia has laundered money and made investments with the complicity of the church.”

Reform-minded Francis has not been afraid to tackle the Vatican’s burgeoning problems, including clearing out the least effective members of the Curia and firing the entire board of the Vatican Bank. But ministering to the mob might be more challenging. “A gunman from the ‘Ndrangheta will pray and kiss his rosary before shooting someone,” Gratteri says. It will likely take more than a threat from Rome to change the mindset of a mafioso.