Turkey had sought Kaplan's extradition in connection with a 1998 plot to crash an explosives-laden aircraft into the mausoleum of Mustafa Kemal Ataturk, in the capital Ankara.
Metin Kaplan, dubbed the "Caliph of Cologne", arrived in Istanbul on a small private jet late on Tuesday after losing his extradition appeal.
Kaplan made no statement as he was charged with treason and remanded in custody until 20 December.
He will be tried by one of the new special criminal courts established under European Union-inspired reforms.
They replace the state security court system which had charged Kaplan in absentia.
The state security courts, scrapped at the EU's insistence, had been used to try political and security-related crimes.
Vote of confidence
Turkish media hailed Germany's extradition of Kaplan as a vote of confidence in Ankara's political and judicial reforms.
"A great gesture from Germany to Turkey as it tries to enter the EU," said the Aksam daily.
Germany only agreed to Kaplan's extradition after being satisfied he would not face human rights abuses back home.
"I think the Turkish authorities will try to make Kaplan's trial as fair and transparent as possible. It is in Turkey's own interests to do so," said one Ankara-based EU diplomat.
Kaplan has served a four year
sentence in Germany for incitement
Kaplan, who headed a Cologne-based group known as the Kalifatstaat (Caliphate state), has already served a four-year sentence in Germany for incitement, which allegedly led to the death of another Muslim cleric.
Berlin outlawed the Kalifatstaat group as unconstitutional and a threat to democracy in 2001. An appeal to overturn the ban was rejected in October 2003.
Tougher laws for Muslims
Germany introduced tighter laws controlling Muslim organisations after it became a focal point of investigations into the 11 September attacks in the United States.
In Turkey, Kaplan faces charges of "trying to destroy the constitutional order by armed force" which could bring a life sentence if upheld.
Kaplan's organisation holds Kemal Ataturk responsible for what it says are numerous attempts at removing and distorting Turkey's Islamic heritage.