The trio, identified only as 21-year-old Alican T., 28-year-old Filiz G. and 31-year-old Fatih K., allegedly supplied cash for the organisations and campaigned for Jihad, or holy war, on the internet.
They were charged with "supporting the foreign terrorist groups German Taliban Mujahideen and the Islamic Jihad Union (IJU)," an extremist organisation linked to militant Islamist group al-Qaida, prosecutors said in a statement.
Two of them are in custody, while authorities are searching for the 31-year-old.
The 28-year-old suspect is the wife of a German convert to Islam, Fritz Gelowicz, who was sentenced in March 2010 to 12 years in jail for what was described the biggest terror plot in German post-war history.
Gelowicz was a member of a four-man IJU cell, known as the “Sauerland cell” after the region where the three were captured in September 2007.
They had planned to murder US soldiers and citizens in Germany with a series of car bombings, but authorities caught the men red-handed as they were mixing chemicals to make some 410 kilogrammes (900 pounds) of explosives, 100 times the amount used in the 2005 London terrorist bombings that killed more than 50 people.