The three men - two German converts to Islam and a Turk - were arrested last September. They had attended training camps in Pakistan and were stockpiling chemicals to make car bombs, prosecutors had said at the time. Authorities reportedly learned of the second plot thanks to US surveillance of internet communications between Pakistan and Germany.
The alleged plotters, all in their 20s, were believed to belong to the Islamic Jihad Union, a group with links to Al-Qaida.
A spokesman for the prosecutors office declined to give details on what the three had been charged with.
The men had over 700 kilos (1,500 pounds) of hydrogen peroxide, the same chemical used in the 2005 attacks on London's transport system which killed 56 people, prosecutors had said, with the explosive power of 550 kilos of TNT.
Just before police arrested the three, drums containing the chemicals had been moved recently to a holiday home in the Sauerland area in the German state of North Rhine-Westphalia which had been rented under a false name.