Every Friday, just yards from a statue of Bill Clinton with arm aloft in a cheery wave, hundreds of young bearded men make a show of kneeling to pray on the sidewalk outside an improvised mosque in a former furniture store.

The mosque is one of scores built here with Saudi government money and blamed for spreading Wahhabism — the conservative ideology dominant in Saudi Arabia — in the 17 years since an American-led intervention wrested tiny Kosovo from Serbian oppression.

Since then — much of that time under the watch of American officials — Saudi money and influence have transformed this once-tolerant Muslim society at the hem of Europe into a font of Islamic extremism and a pipeline for jihadists.

Kosovo now finds itself, like the rest of Europe, fending off the threat of radical Islam. Over the last two years, the police have identified 314 Kosovars — including two suicide bombers, 44 women and 28 children — who have gone abroad to join the Islamic State, the highest number per capita in Europe.

They were radicalized and recruited, Kosovo investigators say, by a corps of extremist clerics and secretive associations funded by Saudi Arabia and other conservative Arab gulf states using an obscure, labyrinthine network of donations from charities, private individuals and government ministries.

“They promoted political Islam,” said Fatos Makolli, the director of Kosovo’s counterterrorism police. “They spent a lot of money to promote it through different programs mainly with young, vulnerable people, and they brought in a lot of Wahhabi and Salafi literature. They brought these people closer to radical political Islam, which resulted in their radicalization.”

After two years of investigations, the police have charged 67 people, arrested 14 imams and shut down 19 Muslim organizations for acting against the Constitution, inciting hatred and recruiting for terrorism. The most recent sentences, which included a 10-year prison term, were handed down on Friday.

It is a stunning turnabout for a land of 1.8 million people that not long ago was among the most pro-American Muslim societies in the world. Americans were welcomed as liberators after leading months of NATO bombing in 1999 that spawned an independent Kosovo.

After the war, United Nations officials administered the territory and American forces helped keep the peace. The Saudis arrived, too, bringing millions of euros in aid to a poor and war-ravaged land.

But where the Americans saw a chance to create a new democracy, the Saudis saw a new land to spread Wahhabism.

“There is no evidence that any organization gave money directly to people to go to Syria,” Mr. Makolli said. “The issue is they supported thinkers who promote violence and jihad in the name of protecting Islam.”

Kosovo now has over 800 mosques, 240 of them built since the war and blamed for helping indoctrinate a new generation in Wahhabism. They are part of what moderate imams and officials here describe as a deliberate, long-term strategy by Saudi Arabia to reshape Islam in its image, not only in Kosovo but around the world.

Saudi diplomatic cables released by WikiLeaks in 2015 reveal a system of funding for mosques, Islamic centers and Saudi-trained clerics that spans Asia, Africa and Europe. In New Delhi alone, 140 Muslim preachers are listed as on the Saudi Consulate’s payroll.

All around Kosovo, families are grappling with the aftermath of years of proselytizing by Saudi-trained preachers. Some daughters refuse to shake hands with or talk to male relatives. Some sons have gone off to jihad. Religious vigilantes have threatened — or committed — violence against academics, journalists and politicians.

The Balkans, Europe’s historical fault line, have yet to heal from the ethnic wars of the 1990s. But they are now infected with a new intolerance, moderate imams and officials in the region warn.

How Kosovo and the very nature of its society was fundamentally recast is a story of a decades-long global ambition by Saudi Arabia to spread its hard-line version of Islam — heavily funded and systematically applied, including with threats and intimidation by followers.

The Missionaries Arrive

After the war ended in 1999, Idriz Bilalli, the imam of the central mosque in Podujevo, welcomed any help he could get.

Podujevo, home to about 90,000 people in northeast Kosovo, was a reasonably prosperous town with high schools and small businesses in an area hugged by farmland and forests. It was known for its strong Muslim tradition even in a land where people long wore their religion lightly.

After decades of Communist rule when Kosovo was part of Yugoslavia, men and women mingle freely, schools are coeducational, and girls rarely wear the veil. Still, Serbian paramilitary forces burned down 218 mosques as part of their war against Kosovo’s ethnic Albanians, who are 95 percent Muslim. Mr. Bilalli needed help to rebuild.

When two imams in their 30s, Fadil Musliu and Fadil Sogojeva, who were studying for master’s degrees in Saudi Arabia, showed up after the war with money to organize summer religion courses, Mr. Bilalli agreed to help.

The imams were just two of some 200 Kosovars who took advantage of scholarships after the war to study Islam in Saudi Arabia. Many, like them, returned with missionary zeal.

Soon, under Mr. Musliu’s tutelage, pupils started adopting a rigid manner of prayer, foreign to the moderate Islamic traditions of this part of Europe. Mr. Bilalli recognized the influence, and he grew concerned.

“This is Wahhabism coming into our society,” Mr. Bilalli, 52, said in a recent interview.

Mr. Bilalli trained at the University of Medina in Saudi Arabia in the late 1980s, and as a student he had been warned by a Kosovar professor to guard against the cultural differences of Wahhabism. He understood there was a campaign of proselytizing, pushed by the Saudis.

“The first thing the Wahhabis do is to take members of our congregation, who understand Islam in the traditional Kosovo way that we had for generations, and try to draw them away from this understanding,” he said. “Once they get them away from the traditional congregation, then they start bombarding them with radical thoughts and ideas.”

“The main goal of their activity is to create conflict between people,” he said. “This first creates division, and then hatred, and then it can come to what happened in Arab countries, where war starts because of these conflicting ideas.”

From the outset, the newly arriving clerics sought to overtake the Islamic Community of Kosovo, an organization that for generations has been the custodian of the tolerant form of Islam that was practiced in the region, townspeople and officials say.

Muslims in Kosovo, which was a part of the Ottoman Empire for 500 years, follow the Hanafi school of Islam, traditionally a liberal version that is accepting of other religions.

But all around the country, a new breed of radical preachers was setting up in neighborhood mosques, often newly built with Saudi money.

In some cases, centuries-old buildings were bulldozed, including a historic library in Gjakova and several 400-year-old mosques, as well as shrines, graveyards and Dervish monasteries, all considered idolatrous in Wahhabi teaching.

From their bases, the Saudi-trained imams propagated Wahhabism’s tenets: the supremacy of Sharia law as well as ideas of violent jihad and takfirism, which authorizes the killing of Muslims considered heretics for not following its interpretation of Islam.

The Saudi-sponsored charities often paid salaries and overhead costs, and financed courses in religion, as well as English and computer classes, moderate imams and investigators explained.

But the charitable assistance often had conditions attached. Families were given monthly stipends on the condition that they attended sermons in the mosque and that women and girls wore the veil, human rights activists said.

“People were so needy, there was no one who did not join,” recalled Ajnishahe Halimi, a politician who campaigned to have a radical Albanian imam expelled after families complained of abuse.

Threats Intensify

Within a few years of the war’s end, the older generation of traditional clerics began to encounter aggression from young Wahhabis.

Paradoxically, some of the most serious tensions built in Gjilan, an eastern Kosovo town of about 90,000, where up to 7,000 American troops were stationed as part of Kosovo’s United Nations-run peacekeeping force at Camp Bondsteel.

“They came in the name of aid,” one moderate imam in Gjilan, Enver Rexhepi, said of the Arab charities. “But they came with a background of different intentions, and that’s where the Islamic religion started splitting here.”

One day in 2004, he recalled, he was threatened by one of the most aggressive young Wahhabis, Zekirja Qazimi, a former madrasa student then in his early 20s.

Inside his mosque, Mr. Rexhepi had long displayed an Albanian flag. Emblazoned with a double-headed eagle, it was a popular symbol of Kosovo’s liberation struggle.

But strict Muslim fundamentalists consider the depiction of any living being as idolatrous. Mr. Qazimi tore the flag down. Mr. Rexhepi put it back.

“It will not go long like this,” Mr. Qazimi told him angrily, Mr. Rexhepi recounted.

Within days, Mr. Rexhepi was abducted and savagely beaten by masked men in woods above Gjilan. He later accused Mr. Qazimi of having been behind the attack, but police investigations went nowhere.

Ten years later, in 2014, after two young Kosovars blew themselves up in suicide bombings in Iraq and Turkey, investigators began an extensive investigation into the sources of radicalism. Mr. Qazimi was arrested hiding in the same woods. On Friday, a court sentenced him to 10 years in prison after he faced charges of inciting hatred and recruiting for a terrorist organization.

Before Mr. Qazimi was arrested, his influence was profound, under what investigators now say was the sway of Egyptian-based extremists and the patronage of Saudi and other gulf Arab sponsors.

By the mid-2000s, Saudi money and Saudi-trained clerics were already exerting influence over the Islamic Community of Kosovo. The leadership quietly condoned the drift toward conservatism, critics of the organization say.

Mr. Qazimi was appointed first to a village mosque, and then to El-Kuddus mosque on the edge of Gjilan. Few could counter him, not even Mustafa Bajrami, his former teacher, who was elected head of the Islamic Community of Gjilan in 2012.

Mr. Bajrami comes from a prominent religious family — his father was the first chief mufti of Yugoslavia during the Communist period. He holds a doctorate in Islamic studies. Yet he remembers pupils began rebelling against him whenever he spoke against Wahhabism.

He soon realized that the students were being taught beliefs that differed from the traditional moderate curriculum by several radical imams in lectures after hours. He banned the use of mosques after official prayer times.

Hostility only grew. He would notice a dismissive gesture in the congregation during his sermons, or someone would curse his wife, or mutter “apostate” or “infidel” as he passed.

In the village, Mr. Qazimi’s influence eventually became so disruptive that residents demanded his removal after he forbade girls and boys to shake hands. But in Gjilan he continued to draw dozens of young people to his after-hours classes.

“They were moving 100 percent according to lessons they were taking from Zekirja Qazimi,” Mr. Bajrami said in an interview. “One hundred percent, in an ideological way.”

Extremism Spreads

Over time, the Saudi-trained imams expanded their work.

By 2004, Mr. Musliu, one of the master’s degree students from Podujevo who studied in Saudi Arabia, had graduated and was imam of a mosque in the capital, Pristina.

In Podujevo, he set up a local charitable organization called Devotshmeria, or Devotion, which taught religion classes and offered social programs for women, orphans and the poor. It was funded by Al Waqf al Islami, a Saudi organization that was one of the 19 eventually closed by investigators.

Mr. Musliu put a cousin, Jetmir Rrahmani, in charge.

“Then I knew something was starting that would not bring any good,” said Mr. Bilalli, the moderate cleric who had started out teaching with him. In 2004, they had a core of 20 Wahhabis.

“That was only the beginning,” Mr. Bilalli said. “They started multiplying.”

Mr. Bilalli began a vigorous campaign against the spread of unauthorized mosques and Wahhabi teaching. In 2008, he was elected head of the Islamic Community of Podujevo and instituted religion classes for women, in an effort to undercut Devotshmeria.

As he sought to curb the extremists, Mr. Bilalli received death threats, including a note left in the mosque’s alms box. An anonymous telephone caller vowed to make him and his family disappear, he said.

“Anyone who opposes them, they see as an enemy,” Mr. Bilalli said.

He appealed to the leadership of the Islamic Community of Kosovo. But by then it was heavily influenced by Arab gulf sponsors, he said, and he received little support.

When Mr. Bilalli formed a union of fellow moderates, the Islamic Community of Kosovo removed him from his post. His successor, Bekim Jashari, equally concerned by the Saudi influence, nevertheless kept up the fight.

“I spent 10 years in Arab countries and specialized in sectarianism within Islam,” Mr. Jashari said. “It’s very important to stop Arab sectarianism from being introduced to Kosovo.”

Mr. Jashari had a couple of brief successes. He blocked the Saudi-trained imam Mr. Sogojeva from opening a new mosque, and stopped a payment of 20,000 euros, about $22,400, intended for it from the Saudi charity Al Waqf al Islami.

He also began a website, Speak Now, to counter Wahhabi teaching. But he remains so concerned about Wahhabi preachers that he never lets his 19-year-old son attend prayers on his own.

The radical imams Mr. Musliu and Mr. Sogojeva still preach in Pristina, where for prayers they draw crowds of young men who glare at foreign reporters.

Mr. Sogojeva dresses in a traditional robe and banded cleric’s hat, but his newly built mosque is an incongruous modern multistory building. He admonished his congregation with a rapid-fire list of dos and don’ts in a recent Friday sermon.

Neither imam seems to lack funds.

In an interview, Mr. Musliu insisted that he was financed by local donations, but confirmed that he had received Saudi funding for his early religion courses.

The instruction, he said, is not out of line with Kosovo’s traditions. The increase in religiosity among young people was natural after Kosovo gained its freedom, he said.

“Those who are not believers and do not read enough, they feel a bit shocked,” he said. “But we coordinated with other imams, and everything was in line with Islam.”

A Tilt Toward Terrorism

The influence of the radical clerics reached its apex with the war in Syria, as they extolled the virtues of jihad and used speeches and radio and television talks shows to urge young people to go there.

Mr. Qazimi, who was given the 10-year prison sentence, even organized a summer camp for his young followers.

“It is obligated for every Muslim to participate in jihad,” he told them in one videotaped talk. “The Prophet Muhammad says that if someone has a chance to take part in jihad and doesn’t, he will die with great sins.”

“The blood of infidels is the best drink for us Muslims,” he said in another recording.

Among his recruits, investigators say, were three former civilian employees of American contracting companies at Camp Bondsteel, where American troops are stationed. They included Lavdrim Muhaxheri, an Islamic State leader who was filmed executing a man in Syria with a rocket-propelled grenade.

After the suicide bombings, the authorities opened a broad investigation and found that the Saudi charity Al Waqf al Islami had been supporting associations set up by preachers like Mr. Qazimi in almost every regional town.

Al Waqf al Islami was established in the Balkans in 1989. Most of its financing came from Saudi Arabia, Qatar, Kuwait and Bahrain, Kosovo investigators said in recent interviews. Unexplained gaps in its ledgers deepened suspicions that the group was surreptitiously funding clerics who were radicalizing young people, they said.

Investigators from Kosovo’s Financial Intelligence Unit found that Al Waqf al Islami, which had an office in central Pristina and a staff of 12, ran through €10 million from 2000 through 2012. Yet they found little paperwork to explain much of the spending.

More than €1 million went to mosque building. But one and a half times that amount was disbursed in unspecified cash withdrawals, which may have also gone to enriching its staff, the investigators said.

Only 7 percent of the budget was shown to have gone to caring for orphans, the charity’s stated mission.

By the summer of 2014, the Kosovo police shut down Al Waqf al Islami, along with 12 other Islamic charities, and arrested 40 people.

The charity’s head offices, in Saudi Arabia and the Netherlands, have since changed their name to Al Waqf, apparently separating themselves from the Balkans operation.

Asked about the accusations in a telephone interview, Nasr el Damanhoury, the director of Al Waqf in the Netherlands, said he had no direct knowledge of his group’s operations in Kosovo or the Balkans.

The charity has ceased all work outside the Netherlands since he took over in 2013, he said. His predecessor had returned to Morocco and could not be reached, and Saudi board members would not comment, he said.

“Our organization has never supported extremism,” Mr. Damanhoury said. “I have known it since 1989. I joined them three years ago. They have always been a mild group.”

Unheeded Warnings

Why the Kosovar authorities — and American and United Nations overseers — did not act sooner to forestall the spread of extremism is a question being intensely debated.

As early as 2004, the prime minister at the time, Bajram Rexhepi, tried to introduce a law to ban extremist sects. But, he said in a recent interview at his home in northern Kosovo, European officials told him that it would violate freedom of religion.

“It was not in their interest, they did not want to irritate some Islamic countries,” Mr. Rexhepi said. “They simply did not do anything.”

Not everyone was unaware of the dangers, however.

At a meeting in 2003, Richard C. Holbrooke, once the United States special envoy to the Balkans, warned Kosovar leaders not to work with the Saudi Joint Relief Committee for Kosovo, an umbrella organization of Saudi charities whose name still appears on many of the mosques built since the war, along with that of the former Saudi interior minister, Prince Naif bin Abdul-Aziz.

A year later, it was among several Saudi organizations that were shut down in Kosovo when it came under suspicion as a front for Al Qaeda. Another was Al-Haramain, which in 2004 was designated by the United States Treasury Department as having links to terrorism.

Yet even as some organizations were shut down, others kept working. Staff and equipment from Al-Haramain shifted to Al Waqf al Islami, moderate imams familiar with their activities said.

In recent years, Saudi Arabia appears to have reduced its aid to Kosovo. Kosovo Central Bank figures show grants from Saudi Arabia averaging €100,000 a year for the past five years.

It is now money from Kuwait, Qatar and the United Arab Emirates — which each average approximately €1 million a year — that propagates the same hard-line version of Islam. The payments come from foundations or individuals, or sometimes from the Ministry of Zakat (Almsgiving) from the various governments, Kosovo’s investigators say.

But payments are often diverted through a second country to obscure their origin and destination, they said. One transfer of nearly €500,000 from a Saudi individual was frozen in 2014 since it was intended for a Kosovo teenager, according to the investigators and a State Department report.

Al Qaeda and other terrorist organizations were still raising millions from “deep-pocket donors and charitable organizations” based in the gulf, the Treasury under secretary for terrorism and financial intelligence, David S. Cohen, said in a speech in 2014 at the Center for a New American Security.

While Saudi Arabia has made progress in stamping out funding for Al Qaeda, sympathetic donors in the kingdom were still funding other terrorist groups, he said.

Today the Islamic Community of Kosovo has been so influenced by the largess of Arab donors that it has seeded prominent positions with radical clerics, its critics say.

Ahmet Sadriu, a spokesman for Islamic Community of Kosovo, said the group held to Kosovo’s traditionally tolerant version of Islam. But calls are growing to overhaul an organization now seen as having been corrupted by outside forces and money.

Kosovo’s interior minister, Skender Hyseni, said he had recently reprimanded some of the senior religious officials.

“I told them they were doing a great disservice to their country,” he said in an interview. “Kosovo is by definition, by Constitution, a secular society. There has always been historically an unspoken interreligious tolerance among Albanians here, and we want to make sure that we keep it that way.”

Families Divided

For some in Kosovo, it may already be too late.

Families have been torn apart. Some of Kosovo’s best and brightest have been caught up in the lure of jihad.

One of Kosovo’s top political science graduates, Albert Berisha, said he left in 2013 to help the Syrian people in the uprising against the government of President Bashar al-Assad. He abandoned his attempt after only two weeks — and he says he never joined the Islamic State — but has been sentenced to three and a half years in prison, pending appeal.

Ismet Sakiqi, an official in the prime minister’s office and a veteran of the liberation struggle, was shaken to find his 22-year-old son, Visar, a law student, arrested on his way through Turkey to Syria with his fiancée. He now visits his son in the same Kosovo prison where he was detained under Serbian rule.

And in the hamlet of Busavate, in the wooded hills of eastern Kosovo, a widower, Shemsi Maliqi, struggles to explain how his family has been divided. One of his sons, Alejhim, 27, has taken his family to join the Islamic State in Syria.

It remains unclear how Alejhim became radicalized. He followed his grandfather, training as an imam in Gjilan, and served in the village mosque for six years. Then, two years ago, he asked his father to help him travel to Egypt to study.

Mr. Maliqi still clings to the hope that his son is studying in Egypt rather than fighting in Syria. But Kosovo’s counterterrorism police recently put out an international arrest warrant for Alejhim.

“Better that he comes back dead than alive,” Mr. Maliqi, a poor farmer, said. “I sent him to school, not to war. I sold my cow for him.”

Alejhim had married a woman from the nearby village of Vrbice who was so conservative that she was veiled up to her eyes and refused to shake hands with her brother-in-law.

The wife’s mother angrily refused to be interviewed. Her daughter did what was expected and followed her husband to Syria, she said.

Secretly, Alejhim drew three others — his sister; his best friend, who married his sister; and his wife’s sister — to follow him to Syria, too. The others have since returned, but remain radical and estranged from the family.

Alejhim’s uncle, Fehmi Maliqi, like the rest of the family, is dismayed. “It’s a catastrophe,” he said.