Party leaders called for the delegates who met in Berlin to support plans by the ruling coalition of conservatives and liberals to abandon nuclear energy by 2022 - despite Green demands for nuclear to be abandoned by 2017.
Leaders say the government has adopted key wishes of the ecology party, which has demanded from its inception that Germany shutter its nuclear power plants.
"We have achieved a real victory after decades of struggle," said Claudia Roth, Green Party co-chair, in front of 500 delegates.
But for many in the grassroots of the party, the government's plans are not fast enough. The party believes Germany can be non-nuclear by 2017, five years before Chancellor Angela Merkel's government plans to turn off the final nuclear switch. Some Green members have also worried about handing the conservatives a victory on the nuclear issue.
Gesine Agena, the spokesperson for the Greens' youth wing, warned strongly in a speech against supporting the government's plans. She said Merkel had not negotiated with the Greens about the nuclear pull-out, but merely presented its fully-formed plan to the party.
She said that central demands of the Greens - such as an end to research on a deep repository nuclear waste storage facility at Gorleben, stronger safety standards and the quickest possible exit from all nuclear energy programs – are not part of the proposed amendments to German law.
In addition, Agena said, there were no guarantees that the government coalition would not simply renage on its promise to close down the nuclear plants.
Her speech received long, sustained applause - but at the end of the day delegates voted to support the leadership and back the government plan which will come before parliament this Thursday.
The German government decided last month to close all of Germany's 17 reactors by 2022, reversing a decision made last year to extend their life span. The move followed Japan's nuclear disaster, which increased already strong resistance within Germany to nuclear power.