The arrest of Syrian national Zoher J. took place at his home in Lower Bavaria on Wednesday, with police also searching the suspect's apartment.
Prosecutors allege that Zoher J. was a member of Jabhat al-Nusra and Isis, both of which are terror organizations operating in Syria. He is also accused of breaching German laws on the possession of weapons of war.
The prosecutors stress that the arrest is not connected to the bomb attack on the Borussia Dortmund team bus on Tuesday evening.
Zoher J. is charged with having set up a fighting unit loyal to Jabhat al-Nusra - an al-Qaeda linked jihadi organization - at some point in 2011.
The young Syrian then led a fighting unit in the east Syrian city of Raqqa before it fell to Isis. Afterwards he joined the radical organization and became a member of their “secret service.”
By August 2015 he had arrived in Germany, prosecutors say, from where he repeatedly travelled to Greece to recruit members for terror cells in Greek refugee camps.
His other task was to coordinate the terror cells which had already been established in Europe in order to see their terror plots through to completion, prosecutors allege.