On June 28 this year, Italian police arrested a silver-haired priest, Monsignor Nunzio Scarano, in Rome. The cleric, nicknamed Monsignor Cinquecento after the €500 bills he habitually carried around with him, was charged with fraud and corruption, together with a former secret service agent and a ­financial broker. All three were suspected of attempting to smuggle €20m by private plane across the border from Switzerland.

Prosecutors alleged that the priest, a former banker, was using the Institute for Religious Works – the formal name for the Vatican’s bank – to move money for businessmen based in the Naples region, widely regarded in Italy as a haven of organised crime. Worse still, Scarano (who, together with the other men, has denied any wrongdoing) had until only a month earlier been head of the accounting department at the Administration of the Patrimony of the Apostolic See, the treasury of the Vatican.

The arrest, and the headlines that screamed across the Italian press, was the latest shock for the Holy See. The year had already witnessed an emotional upheaval in the church with the resignation in February of the aged Pope Benedict XVI – the first time in 700 years a pope had stepped down voluntarily. But this new crisis demanded cold, hard resolve. For regulators and politicians in Europe who had pushed for change in the Vatican’s scandal-plagued bank over the previous four years – from the Bank of Italy under Mario Draghi to officials in Mario Monti’s government and in Brussels – it served as evidence of their concerns. Those worries also jolted a number of international financiers determined to press for reform.

In early July, Peter Sutherland, non-executive chairman of Goldman Sachs International and the former attorney-general of Ireland, flew into Vatican City. His mission – although described by some insiders as simply a “bit part” in the wider drive for change – was an illuminating one. Sutherland, a practising Catholic and an unpaid consultant to the Vatican’s treasury, had been asked by reformers in the church to speak with the council of cardinals, the most senior advisers to the pope. His message to the men who filed into a room near Doma Santa Marta, the plain-fronted residence of Pope Francis, was respectful but direct.

The banker, who declined to comment for this story, added his voice to the many in and outside the church asking the world’s smallest city-state to change its ways. “Transparency is important and necessary,” Sutherland said, according to two people who were informed of proceedings in the closed-door meeting.

The cardinals, known for long, contemplative consultations, were surprisingly receptive, said one of those informed. After a decade of paedophilia scandals, the allegations of financial impropriety seemed set to unleash another storm of criticism and had to be addressed. Outside auditors as well as financial risk consultants were already coming into the Vatican but the arrest of Scarano made the case for reform unavoidable. “We cannot have any more scandal. It is so shameful,” a senior member of the Vatican’s financial administration said.

Audio Slideshow How the Vatican bank ended up as a financial penitent The Financial Times has investigated the extent of the mismanagement at the Vatican bank. In this audio slideshow, find out how the scandal erupted and what has been done to help strengthen the bank.

How God’s bank ended up as a financial penitent this year is a bracing chapter in the history of financial reforms that have swelled up in the aftermath of the 2008 credit crisis. Untouchable havens such as Switzerland and Liechtenstein were forced to open their chocolate-box palaces to the probes of international regulators. This year the power of the popes was challenged.

The FT interviewed two dozen bankers, lawyers, regulators and Catholic insiders over 11 months to understand how the murky operations of a bank with €5bn in assets, and which says its aim is to serve the global mission of the Catholic Church, had unnerved bankers, regulators and governments across Europe and the US.

The reforms now under way at the Vatican have come about in part because of the pressure brought to bear by banks such as Deutsche Bank, JPMorgan and UniCredit, all of which found themselves in the sights of regulators because of their business relationships with the Holy See. About three dozen banks, including some of the world’s biggest financial institutions, were for years “correspondent” banks to the Vatican, providing services when the pope’s business went beyond the boundaries of Vatican City. As with other institutional clients, the banks gave the Vatican access to foreign financial markets. Correspondent banks moved as much as €2bn a year from the Vatican’s bank to other accounts across the globe, according to a Vatican spokesman. It was the bankers’ fear of being tarnished by their links with the Vatican bank after the credit crisis – and fears of fines from emboldened regulators – that led them to take steps that forced it to clean up its act.

Appeal for transparency: Peter Sutherland, non-executive chairman of Goldman Sachs International and unpaid consultant to the Vatican’s treasury

Several financial professionals talked in detail to the FT about their dealings with Vatican staff and provided documents about the bank’s structure. None wanted to speak on the record, citing sensitivities in both their banking and religious worlds. All told the FT that they were speaking out in order to help the bank keep to its programme of reform.

Senior executives from some correspondent banks had been questioned by regulators over the past two years and several had the same refrain about their dealings with the Vatican bank: it operated unlike any other bank they had encountered. Some who spoke to the FT reinforced what later emerged from reports by European officials on the bank’s workings. There were surprisingly few checks and balances on cash flow – and far less documentation than expected. The staff was small – 112 people, largely Italian until this year, with cardinals acting as supervisors. Many of the staff seemed unversed in customer due diligence, according to some. “They would not answer basic [Know Your Client] requests,” a senior manager at an international bank says.

The Institute for Religious Works issued its first annual report in early October, which showed that the bank has 19,000 clients, from around the world, 33,000 accounts and €5bn in assets. Few loans are made; the bank holds deposits, transfers money and makes investments. Half the bank’s clients come from religious orders; another 15 per cent are Holy See institutions, 13 per cent are cardinals, bishops and clergy, 9 per cent are from Catholic dioceses around the world. The rest of the clients are split among those who have, or should have, some “affiliation to the Catholic Church”, the report says.

Vatican insiders also revealed that the bank is awash in donations and cash, from Sunday collections and charitable giving. As much as 25 per cent of the bank’s business is done in cash – a feature that regulators said raised red flags for money laundering. About a third of its business comes from donations rooted in charities.

Laura Pedio, a Milan anti-Mafia prosecutor who specialises in white-collar crime, was one of the few sources willing to speak publicly to the FT. Pedio, who had been investigating the bankruptcy of a Catholic hospital in 2011 and needed access to Vatican bank information, said she was astonished to find a complex system of proxies, the authorisations given to representatives to execute transactions on behalf of often unidentified beneficial account holders.

She found multiple people often had proxies but details about the proxy holders were apparently not recorded anywhere in the bank. Some, she said, could be verbally identified by only a few people within the Vatican bank. There was, she said, literally no way to force an answer. “The issue was always: ‘Who is the ultimate beneficiary of this account?’” she says.

One adviser to the Vatican, who lives hundreds of miles from the marble colonnades of Rome, says the pursuit by prosecutors and regulators of the Vatican created a shift in mood among bankers to the Holy See. Under pressure themselves from a clampdown by European regulators, the banks were no longer open for business with a secretive Vatican. “There was a no-nonsense approach from the correspondent banks,” this adviser says. “‘We are not here to cover the ass of the Vatican.’”

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Vatican City, a sovereign state that fiercely guards its privacy, has some of the trappings of a small town, with a supermarket, pharmacy, petrol station and a post office within its borders. But its hometown bank has the plummiest of addresses: the Apostolic Palace.

Popes Benedict and John Paul II both had their bedrooms two floors above the bank. An elevator was installed in the Apostolic Palace for John Paul II when he became too infirm to take the stairs. The elevator’s ground-floor entrance is next to the back door of the bank. (Pope Francis has opted for a less palatial residence, notably on the opposite side of Vatican City to the bank.)

Debate about what the popes knew about who came and went through the bank’s doors has occupied generations of Vatican watchers. The bank’s forerunner was created in 1887 as “an administration” to gather and use money for religious works. In 1942, in the chaotic war years, Pope Pius XII gave it a new name and a clear banking purpose.

The Institute for Religious Works was to provide for “the custody and the administration of monies (in bonds and cash) and properties transferred or entrusted to the Institute itself by fiscal or legal persons for the purposes of religious works, and works of Christian piety”. In the decades that followed, questions about some of that work – notably relationships and business deals examined by David Yallop in his 1984 bestseller, In God’s Name – would stir intrigue about possible Mafia connections. A 1996 book, His Holiness by Marco Politi and Carl Bernstein, offered a more benevolent view of Vatican cash flow in the 1980s: Pope John Paul II had systemically sent money to Solidarity, the Polish resistance movement, through a papal discretionary account, in an effort to break the back of communism in eastern Europe.

Mafia victim: Roberto Calvi?

The most infamous publicity surrounded revelations about the Vatican bank’s dealings with Milan’s Banco Ambrosiano, one of the most high-profile bank collapses in Italy’s history. The Vatican bank was Banco Ambrosiano’s main shareholder. After its demise in 1982, Banco Ambrosiano’s chairman, Roberto Calvi, was found hanged under London’s Blackfriars Bridge. Prosecutors in Rome concluded that he was killed by the Sicilian Mafia but no one has ever been convicted of his murder.

In recent years, the bank has again featured in media reports for its funding of religious and humanitarian activities across the world. Former and current Vatican officials have confirmed to the FT that the bank has been used to channel cash, often secretly or with ­limited information given to correspondent banks, to vulnerable Christian groups in Cuba and Egypt.

But Vatican insiders, bankers and prosecutors admit that a system aimed at quickly getting money to difficult places has also potentially been open to abuse by tax cheats and by organised crime. “The issue is that once you start doing opaque transactions in an institution, people don’t know where to draw a line and to stop. What started in effect with moving money to Poland got out of control,” says a senior European banker at a US bank with a longstanding relationship with the Vatican. “There were no rules,” a Vatican insider commented. “So if you add to that someone with a criminal [motivation], you are finished.”

Up until 2008, according to one former senior Vatican banker, regulation of the Vatican bank was “indulgent”. This person says that no pressure was brought to bear on the Vatican to clean up its act either by regulators overseeing its correspondent banks or by officials within the Holy See.

But the euro crisis changed all that. Pressure from the Organisation for Economic Co-operation and Development, Europe’s Financial Stability Board and the Financial Action Task Force led to a crackdown on states that failed to comply with international rules. At the same time, prosecutors in Rome were probing suspicious transactions that appeared to be emanating out of the Holy See into the Italian banking system. Their focus was a branch of UniCredit, Italy’s largest bank by assets, that sits on the road leading up to Vatican City.

Flow of funds: Pope John Paul II is said to have used the Vatican bank to channel money to Poland's Solidarity movement

A routine Bank of Italy anti money-laundering investigation at the branch had stumbled upon inconsistencies in its dealings with the Vatican bank, and it referred the issue to Rome prosecutors. According to a source familiar with the matter, payment slips from unnamed holders of Vatican bank accounts were found in the branch, ringing alarm bells for anti-money laundering investigators. The investigation was shelved later that year but not without consequences for the Vatican. UniCredit says it cut off all contact with the Holy See. It would not be the last bank to do so.

Forcing change was a challenge. Part of the problem was that the European Union had no regulatory power over the Vatican’s bank. So it was decided that the Bank of Italy, at the time headed by Draghi, would put pressure on the banks that did business with the Vatican. A former Italian minister with direct knowledge says: “That is the way you do it in these situations, when you have a state that you do not have regulatory powers over but you want to enforce changes. You make their life very difficult. You tell the banks they are not allowed to do business with them.”

By 2009, the Vatican bank was caught in various financial crosshairs. As prosecutors continued their line of questioning, the Bank of Italy was putting on the pressure by making life tough for the correspondent banks, according to several people with direct knowledge of events.

The Vatican, with an increasingly frail Benedict at the helm, tried to put its own stamp on the probes by appointing a well-connected conservative banker, Ettore Gotti Tedeschi, to take over the presidency of the bank. It also made a request to the Council of Europe for an investigation by Moneyval, the council’s Committee of Experts on the Evaluation of Anti-Money Laundering Measures and the Financing of Terrorism. Pope Benedict even gave his blessing to the creation of a financial supervisor within the walls of the Vatican.

Gotti Tedeschi was well known to the central bank. He was the head of Banco Santander in Italy and considered to be the right-hand man of Santander’s powerful executive chairman Emilio Botín in the country. He also sat on the board of Italy’s giant state financing agency, Cassa Depositi e Prestiti. But according to people familiar with the events, Gotti Tedeschi was viewed with distrust among some members of the council of cardinals which he tried to encourage to be more transparent. Personal battles with the Vatican hierarchy took their toll as well: in May 2012 he was ejected from the presidency after a no-confidence vote by the board. He even faced criminal charges that were later dropped after an investigation by Italian prosecutors.

That year, correspondent banks also grew increasingly worried. The Vatican’s failure to comply with international anti-money laundering rules had the potential to affect their own businesses. As regulators cracked down on tax cheats in offshore havens such as Switzerland, the banks feared regulators would turn on them for working with a Vatican that was still guarding its own banking secrets.

In March 2012, JPMorgan closed the bank account it held for the Vatican because the Vatican bank was providing insufficient information about funds that it was asking the US bank to move around the world, according to two sources at two different financial institutions. Other banks started to push back against the Vatican. “We would say, ‘We need to answer the regulator on this matter.’ They would say, ‘We answer to God,’” says another manager at a large European bank.

The EU’s Moneyval reinforced the sense of embattlement at the Vatican with its report in July 2012. Moneyval said that the Financial Information Authority, the regulator set up with Pope Benedict’s blessing, lacked the legal powers and independence needed to monitor and sanction the Vatican’s financial institutions. It had found that the regulator had no clear right to demand access to books or information. The Vatican bank was deemed to be compliant or largely compliant on only nine out of 16 core standards.

Moneyval provided ammunition for other banks and the crunch came when regulators turned to Deutsche Bank, the German financial powerhouse. Its Italian subsidiary had managed the Vatican City’s 80 cash machines and credit card payment services since 1997. In the summer of 2012, the Bank of Italy began questioning Deutsche about whether it possessed a licence to operate cash machines for the Vatican state. The central bank said that the Vatican was not compliant with international rules; was Deutsche breaking the law by servicing the ATMs? The Bank of Italy then sent another letter, seen by the FT, that ordered Deutsche Bank to close its accounts with the Vatican bank by the end of the year.

Deutsche did what regulators had hoped it would. On January 1 2013, a peak holiday time, there were no ATMs functioning anywhere inside Vatican City. Lines of visitors to the Sistine Chapel were unable to enter unless they paid in cash. “The message sent was simple: if you want to participate in the modern world, you have to adopt modern rules,” says a senior banker at another correspondent bank.

In the waning days of his papacy, Benedict made appointments that would help steer the church towards some sort of financial resolution. He appointed Rene Bruelhart, a Swiss lawyer who made his name as the head of Liechtenstein’s ­financial intelligence unit, as head of the Vatican’s financial regulator. Among the pontiff’s last official decrees was to appoint a new Vatican bank chief, Ernst von Freyberg, a mergers and acquisitions banker and aristocratic German who in his spare time led pilgrims to the healing waters of Lourdes.

Bruelhart, the younger of the two men, was involved in the return of assets owned by the regime of Saddam Hussein to the new Iraqi government. He also helped to uncover the Siemens contract scandal of 2006, which involved bribery of government officials. This legal profile, combined with his crisp good looks, led some in the media to dub the 41-year-old the James Bond of the financial world.

Pope Francis celebrates mass in St Peter’s Square in October

Bruelhart worked swiftly to restore ATM services in Vatican City. By February 12, he had engaged Aduno Group, a Swiss ­company, to take over operation of the cash machines, neatly circumventing Italian and EU regulatory pressures.

In March 2013, there was a new pope – a Jesuit evoking the poverty and humility of St Francis of Assisi – and he quickly set a tone on financial correctness. Pope Francis spoke out against the “idolatry of money”, “all-encompassing corruption” and “tax evasion that had reached global dimensions”. Behind the scenes, he sent out another sign: Pope Francis moved his ­personal residence away from the Apostolic Palace and the Vatican bank.

Francis also began issuing papal decrees that helped speed inspections and made changes within the upper ranks of the cardinals. According to Bank of Italy sources, the new pope “marked important steps toward real reform of the legal and institutional framework”. Backed by Francis, the Financial Information Authority was strengthened with broader powers of supervision.

The pope had also asked for a review of the bank’s activities and appointed two boards made up of senior clergy and lay bankers to give advice regarding the future of the institution so that “it was in harmonization with the mission of the Catholic Church”, according to Vatican statements.

So far, Bruelhart and von Freyberg have complemented each other in their approach to reform, insiders say. Bruelhart quickly set up a crisis management team to review accounts and track money transfers. Within months of the two financial outsiders arriving, Sutherland flew in from London to discuss the virtues of transparency with the cardinals.

Before the meeting, Sutherland went into the dining hall of the Doma Santa Marta. Pope Francis was also there, eating breakfast, according to a witness. “I could not believe my eyes. I thought this is impossible,” says this person. “The pope in one corner and one of the world’s best-known bankers in the other.”

From left: Ernst von Freyberg, Vatican bank chief, and Rene Bruelhart, head of the Vatican’s financial regulator

By this summer, von Freyberg had sought out Promontory Financial, a global risk-control group that specialises in regulatory and compliance issues. Promontory’s contract, according to von Freyberg, costs “well above seven digits”.

On a bright morning in late October, nine Promontory Financial employees sat in an office beneath a painting of the crucifixion of Christ, sorting through computer scans of account holders’ passports. They were manually and methodically cross-checking the names and faces with newly filled-in bank forms. Promontory employees now comprise 25 per cent of the staff of the Vatican bank, according to the Vatican.

Next door sat Rolando Marranci, a former chief financial officer for BNP Paribas’s Italian subsidiary and now the Vatican bank’s new director-general. He was hired in the wake of the arrest of Scarano, the Vatican accountant.

By next year, these new employees are expected to have closed hundreds of bank accounts listed in the Vatican ledgers, according to people familiar with the situation. Vatican bank officials say it will take well into next year to review them all. Accounts are being targeted when a client has been found to no longer have links to the Holy See. Where accounts are missing basic information or a client is found not to have such links, those accounts have been handed over to Bruelhart and his team. Bruelhart then judges whether to close these accounts when he reviews them in the light of the Vatican’s new, stricter anti-money laundering rules, according to bank insiders.

Both Bruelhart and von Freyberg have tried to calm internal fears about the Vatican’s suspected links to money laundering. Its volume of transactions – about €2bn in and out annually – is too small to be much of a threat, say people familiar with their thinking. But suspicions remain that the bank may have been a refuge for tax cheats from Italy, which European officials admit has a problem with tax evasion.

Bankers familiar with the transition between popes describe the past year as marking an epochal change. The Vatican hierarchy is taking steps to appoint experienced regulators to head a new, prudential supervisor, Vatican insiders say. Big Four auditors are looking at its accounts. The Vatican bank staff was once dominated by Italians; now it is opening its doors to foreign bankers with global experience. The clean-up has also extended to enhanced oversight of the Vatican’s treasury, known as the Administration of the Patrimony of the Apostolic See (Apsa), which controls the Catholic Church’s real estate portfolio and oversees holdings of government bonds. Sutherland and fellow international financier Bob McCann, chief executive of UBS Americas, are listed as two of five “consultors” or advisers at Apsa, according to a 2013 Vatican directory. The Vatican announced in October that its consultors would become part of a newly created supervisory board. Neither man would respond to questions about the board but there is work to be done there as well.

A handful of current accounts was recently discovered within Apsa – to the surprise of auditors and Vatican officials – and they are in the process of being moved to the Vatican bank, according to people with direct knowledge of the events. The very existence of these accounts is yet another sign, these people say, of how the financial system operated for years without any clear rules.

More changes are ahead. Bruelhart has signed a memorandum of understanding to swap information on suspicious transactions with the US, Italy, Spain, Belgium, the Netherlands and Slovenia, and it has another 15 to 20 in the pipeline. He has also reached out to the Egmont Group, an informal network of national financial intelligence units that swaps information about suspicious transactions, according to the Vatican.

There is a cautious sense of optimism among technical ­advisers in Rome and beyond. But they admit that there is still tension between the high priests of finance and the Vatican. “It is a case of political will in the end,” says an adviser to the bank. “Though what is happening here is surprisingly unpolitical. This is about IT and handbooks, and staff training and processes and fact-checking.”

Pope Francis in October in St Peter’s Square

How far the Vatican reforms go depends on the man at the top. Named after a saint who was plain-spoken and happy with simple pursuits, Pope Francis’s approach so far has inspired the bank investigators to work some long and late hours. For them, his early reflections on what banking should be – in this bejewelled city of saints and sinners, or anywhere in the world – is worthy of some meditation. “Some say the best thing is to have a bank, others say it should be a relief fund, other recommend it be closed down,” Pope Francis said in July. “I trust the work the [Vatican bank] team is doing . . . But whether it’s a bank, a fund, a whatever, it should be based on transparency and honesty.”

In Italy, there is a sense that Pope Francis, a native of Argentina, was chosen in part because he was an outsider. He understands that the Vatican’s insular nature has hurt the image of the Catholic Church and raised concerns about its relevance. His papacy will be a mission to prove that the church remains a touchstone for morality – and, to some observers, he has defined the bank scandal as an opportunity.

Massimo Faggioli, an academic and author from Bologna who has studied the Vatican for the past 20 years, says that other pontiffs in his lifetime had no reason to think that the bank was important to the outside world. But now it is – and Francis, by speaking out about it early, has signalled its importance. “Pope John Paul II didn’t touch the bank because it served his purpose of funding Solidarity from the Vatican. Pope Benedict did not touch it because he had no interest in controlling it,” says Faggioli. “Pope Francis is different because he knows the damage that has been done to the credibility of the church by this very small bank and its history of scandals.”

More questions of modernity also will test the church: ongoing paedophilia scandals, the role of women, the possibility that priests may marry. For now it seems the newest occupant of St Peter’s throne wants the church to set an example and do what most everyday people must: get its finances straight.

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Rachel Sanderson is the FT’s Milan correspondent. To comment on this article, please email magazineletters@ft.com

This article was amended on December 16 to correctly reflect the context of Banco Ambrosiano’s collapse