The move comes after police searched 53 properties on Wednesday belonging to Islamic Center Hamburg (IZH) in eight different regions.
Interior Minister Nancy Faeser said: “Today, we banned the Islamisches Zentrum Hamburg, which promotes an Islamist-extremist, totalitarian ideology in Germany.
“This Islamist ideology is opposed to human dignity, women’s rights, an independent judiciary, and our democratic government.”
She added that “this ban absolutely does not apply to the peaceful practice of the Shiite religion.”
Shia make up roughly 10% of all Muslims, and globally their population is estimated between 154 million and 200 million, according to a 2009 report from the Pew Research Center.
In addition to the IZH, which includes one of the oldest mosques in Germany known for its turquoise exterior, its subgroups in Frankfurt, Munich, and Berlin were also banned.
The ministry reported that, as a result of the clampdown, four Shiite mosques will also be closed.
It added that evidence from an earlier search conducted in November of 55 properties provided the basis for Wednesday’s ban.
The ministry said: “The IZH acted as a direct representative of Iran’s Supreme Leader and sought to bring about an Islamic revolution in Germany that would create theocratic rule [...] the IZH promotes anti-Semitism and the Iran-backed militant group
Hezbollah, which is also banned.”