Necati Coskun, the head of the Eyup Sultan mosque association in the town of Weil am Rhein, said unknown assailants threw at least four devices at the building, causing minor damage.
The latest attack has taken place amid a surge in anti-Muslim sentiment in Germany.
Coskun said members of the community were worried about growing anti-Muslim feeling.
"For many years we lived together peacefully; we have never done harm to anyone. Our mosques never interfered in politics, always remained neutral,” he said.
"We hope that the perpetrators will be swiftly arrested and brought to justice,” Coskun added.
The mosque’s security cameras captured images of a group of five people throwing devices at the building. Police have appealed to the public for help in identifying the suspects.
Source: Anadolu Agency