Police raided seven buildings in the northern port city of Hamburg, where the Muslim Interaktiv group was based, as the ban was announced.
"We will not allow organisations such as 'Muslim Interaktiv' to undermine our free society with their hatred... and attack our country from within," Interior Minister Alexander Dobrindt, of the centre-right CDU/CSU bloc, said.
The association came under fire in April 2024 during a rally in Hamburg where more than 1,200 people demonstrated, denouncing Germany's allegedly Islamophobic policies.
Signs carried at the rally included some that read "the caliphate is the solution", which made headlines across the country and prompted a heated national debate.
The group, also accused of rejecting women's rights and promoting hatred of Israel, will now be dissolved and its assets confiscated, according to the ministry.
The city of Hamburg said the group, founded in 2020, was active online and denounced what they said were its claims that the "entire Muslim community" was being rejected by politicians and society.
Hamburg's interior minister, Andy Grote of the centre-left Social Democrats (SPD), welcomed the ban and said that authorities had "eliminated a dangerous and very active Islamist group".
Police on Wednesday also searched buildings in Berlin and the western state of Hesse as part of investigations into two other groups, "Generation Islam" and "Realitaet Islam".
Germany has previously banned a number of Muslim organisations, such as the NGO Ansaar, which was accused in 2021 of financing Islamist terrorism under the guise of charitable work.
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