Refugees at Saalfeld train station after travelling to Germany via Austria and Hungary. PHOTO: TELEGRAPH/CORBIS
But experts suggest the change could be positive for it could broaden outlook, and say fears of radicalism may be overblown.
For a Syrian refugee family, attending Friday prayers in a German mosque can be a headache.
Read: With refugees, German Muslim minority could be Europe's largest
"Most sermons are held in Turkish," said Yasemin El-Menouar, Islam expert at think-tank the Bertelsmann Foundation.
A legacy of Germany's post-war industrial revival, the more than four-million Muslim community is "two-thirds of Turkish origin or culturally Turkish," the researcher told AFP.
In the 1960s and 70s, Turkish construction and factory workers came to participate in the "economic miracle" years.
Today, "even in the second and third generation, Turkish influence is strong," said El-Menouar.
More than 900 mosques are managed by the DITIB, the European arm of the Turkish state secretariat for religious affairs, a key interlocutor for German authorities on matters related to the third largest religion in the country. DITIB declined to comment to AFP.
In these religious communities imams have usually been sent directly by Ankara for over 30 years. Most of the time, they do not speak German, and very often, it is a portrait of Ataturk, the father of modern, secular Turkey, which adorns the walls of the organisation.
All this is worlds away from the religious and historic backgrounds of Muslims who may have fled the Syrian battlefields of Homs or the Iraqi city of Mosul, now in the hands of the Islamic State jihadist group.
"Now they will have to open up to Muslims from other parts of the world," said El-Menouar.
It could be a "stroke of luck," said Mouhanad Khorchide, who holds the Chair on Islam at the University of Munster.
"Islam in Germany will gain in diversity," said Khorchide, who lives under police protection after receiving death threats from radicals.
The number of newcomers is enormous. Of the more than 800,000 new asylum seekers expected in Germany this year, some 80 percent are Muslims, according to the Central Council of Muslims in Germany (ZMD).
More than 161,000 Syrians now live in Germany and the number is expected to grow further, making it the largest Syrian community in Europe.
Some worry about a possible radicalisation of the community, given the influx of people unfamiliar with Western values, from countries where homosexuality may be a crime and gender equality doesn't exist.
Read: Tempers flare in Germany's crowded refugee centres
Young radicals of the Salafist movement have also attempted to "recruit" disoriented young migrants.
But the interior ministry insists the proportion is very small and no cause for alarm as yet.
German intelligence has estimated there are about 7,900 Salafists in Germany. Some have made headlines, for example by forming a "Sharia police" last year to patrol a nightclub area in the western city of Wuppertal.
Chancellor Angela Merkel has repeatedly reminded refugees to respect the principles of a free society and the rule of law.
Germany will continue to be defined by "the constitution, the social market economy, the freedoms of religion and expression," she said in a newspaper interview Monday.
"To the people who come here, we make clear from day one that we have laws and rules that govern communal life which they must follow. Only in this way can Germany be a safe haven to them".
In Berlin, in the 12 asylum homes run by the Workers Welfare (AWO) aid organisation, no religious practice is allowed, a rule meant to preempt potential problems.
Read: Germany celebrates 25 years of unity with call for refugee welcome
"We tell those who ask where there are mosques nearby but we do not authorise any prayers over our loudspeakers," said its chairman Manfred Nowak.
For Khorchide, of Munster University, the major challenge will be the social integration of young refugees.
"If we leave them on the margins of society, if we do not quickly give them the feeling that they are wanted in Germany, then the danger is great that they turn to Salafist and radical movements," he said.
The risk is however diminished by the fact that many have just fled from radical militants in Syria or Iraq, said El-Menouar.
Khorchide agreed.
"Those who lived through the atrocities of the Assad regime or the Islamic State do not want to hear talk of Islamic fighters," he said.
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