The preacher from the Baltic Sea island of Öland received written notification on Tuesday of his expulsion from the teetotaller organization IOGT_NTO.
"The board has decided that your repeated negative comments about homosexuals as a group run counter to IOGT and NTO's founding tenets and policy," wrote the organization's secretary general Stefan Berg, Christian newspaper Världen Idag reports.
Green told the newspaper he was surprised and upset by the ruling.
"Homosexual members are clearly worth more than Christian members," he said, before outlining his fears that IOGT-NTO risked losing face among its Christian supporters.
Åke Green became a household name when he was indicted on hate speech charges following a sermon in Borgholm in 2003 in which he spoke of "sexual perversions" as a "cancerous tumour on the societal body".
Green was convicted of agitating against a sexual group by Kalmar District Court. He was however later cleared by both the Court of Appeal and the Supreme Court.