The event was organized by mainstream Muslim organizations to emphasize that the vast majority of believers reject the group's ideology and its brutal actions in Syria and Iraq.
The head of Germany's Central Council of Muslims, Aiman Mazyek, said the protest Friday was also directed against racism and intolerance in general, citing recent attacks on mosques and synagogues in Europe.
Earlier, German federal prosecutors said they have charged a man and two women with supporting the Islamic State extremist group.
Prosecutors said in a statement the main suspect, 25-year-old Karolina R., a German and Polish citizen, is married to an Islamic State member. Using a middleman, she's accused of providing the group with 1,100 Euros ($1,400) worth of cameras and accessories to produce propaganda videos in October.
Prosecutors said shortly afterward she personally traveled to Syria and delivered three more cameras and 5,000 Euros in cash.
After her return in December, she was accused of sending a further 6,000 euros, some raised with help from the other two people charged, Germans Ahmed-Sadiq M., and Jennifer Vincenza M., both 22.
No last names were released in line with German privacy laws.