The two men, described as dual German-Russian nationals, were detained in Bayreuth on suspicion of spying for Russia, prosecutors say.
Interior Minister Nancy Faeser said authorities had prevented “possible explosive attacks”.
The men are accused of scouting US military facilities and other sites.
The main suspect, Dieter S, has been remanded in pre-trial detention accused of a string of offences, including plotting an explosion, arson and maintaining contact with Russian intelligence.
The second suspect, identified as Alexander J, is accused of helping him since last month to identify potential targets for attack. He was due to appear in court on Thursday.
The Russian ambassador has been summoned by the foreign ministry in Berlin.
