"It wasn't successful and it wasn't worth us continuing, so we made the decision to concentrate on the London stores," said managing director Caroline Gooding.
The three stores in London were growing fast, she claimed, and the business was looking to expand within the M25. "They are very profitable and working well for us," she said. "We are still looking for new sites because we're seeing growth year-on-year up 10% to 15%."
The Hale store closed almost two years to the day after its opening in 2007.
Gooding had admitted last year that it had been difficult to make the concept of an organic supermarket work in Manchester.
"Being in London, I think you can get a bit detached from what's going on in the rest of the country. Opening in Hale's been a steep learning curve," she told the Manchester Evening News.
"Shoppers in Hale care more about local foods. Some will only buy organic but a lot of our customers want to support local producers, even if that food's not certified organic."