Jenica Atwin's departure comes after the Israeli-Palestinian conflict exposed fault lines in the Green party ranks.
Atwin directly challenged party leader Annamie Paul's position on the conflict, saying Paul's call for de-escalation and a return to dialogue between the two was "totally inadequate."
"I stand with Palestine and condemn the unthinkable airstrikes in Gaza. End Apartheid!" Atwin tweeted on May 11.
The day before, Manly tweeted that the removal of Palestinian families from the East Jerusalem neighbourhood of Sheikh Jarrah "is ethnic cleansing."
More recently, the Canadian Press reported that the Green executive committee voted not to renew the contract of one of Paul's senior advisers.
The adviser, Noah Zatzman, had expressed solidarity with Israel in a May 14 social media post that accused many politicians, including unspecified Green MPs, of discrimination and antisemitism, sparking a letter-writing campaign calling for his removal.
Separately, two party executives recently announced they would step down early. One of them was John Kidder, a vice-president on the party's governing body and husband to MP and former leader Elizabeth May.