The agency cited client conflict with Richard Desmond's publishing company Northern & Shell as the reason behind the decision.
Emap is currently holding a pitch for the business. Mother, one of Emap's roster agencies, is thought to be a front-runner for the account.
BMB is currently working on its first campaign for Desmond's newspaper, the Daily Star, which will see it positioned as a source of daily gossip more than a provider of hard news.
Desmond asked BMB to resign the Emap account on the basis that the audiences for the newly positioned Daily Star and Zoo would overlap.
BMB will work closely with Northern & Shell's in-house design team on the new Daily Star campaign.
A spokesman for Zoo said: "We were surprised that BMB had to make this decision and we are obviously disappointed, given that there was no previous indication of conflict and given the time and effort that the Zoo team put into the agency search process.
"However, we are very close to appointing a new agency and will be making an announcement shortly."
In the most recent magazine Audit Bureau of Circulations figures, released in August last year, Zoo increased its sales by 8.8 per cent year on year to 260,000 copies a week. This places it almost 45,000 copies behind IPC Media's Nuts - its main rival in the sector.
In November 2005, Zoo's launch editor, Paul Merrill, left to take up a European role within Emap. He was replaced by Anthony Noguera.
According to December's newspaper ABCs, the Daily Star suffered a 1.98 per cent drop in sales year on year to 779,556 copies.