Some Party members expressed their concern over the new alliance with fellow opposition the Social Democrats.
The Greens say there is a risk that key aspects of their political standpoint may be lost in the collaboration.
The main areas dividing the two parties are the EU, refugee policy and environmental issues.
Meanwhile the Conservative Moderates who head the Centre Left Coalition gather in Stockholm for their EU debate.
Foreign minister Carl Bildt opened the talks by denying rumours that another public vote on the Euro is on the cards.
Sweden will take over the EU presidency next summer.