In her Instagram post she says: “I recently took part in a campaign, which excited me because it celebrated inclusivity.”
She goes on to explain that she is stepping down “with regret” because “the current conversations surrounding it detract from the positive and inclusive sentiment that it set out to deliver”.
It follows accusations that she expressed “anti-Israel” views in a number of tweets from 2014.
Amena had hoped her role would inspire and empower other women who wear headscarves.
Earlier this month, she told Newsbeat: “It’s a platform for diverse voices and women who don’t fit the very narrow mould of beauty.”