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Several hundred well-wishers, including many schoolchildren, lined up in the sunshine to greet the Queen and Philip in Harpurhey, where they toured the The Factory Youth Zone.
The aim of The Factory is to give eight to 21-year-olds "somewhere to go, something to do and someone to talk to".
Similar centres are up and running in Carlisle, Blackburn, Oldham and Wigan, with two more to follow in Wolverhampton and Birkenhead in 2015 thanks to £1million donations each from The Queen's Trust and the St James's Palace Foundation.
The Queen's Trust is also providing a grant of £200,000 towards the development of a Preston Youth Zone.The Queen and Philip later departed for a private lunch ahead of their return home on the Royal Train.
The first engagement of today's Royal visit to Manchester was to officially open the world's "greenest" office building.
The royal party was greeted with enthusiastic cheers from office workers lining the floors overlooking the entrance hall at One Angel Square, the Co-operative Group's new head office in the city.
The firm's £100 million HQ has been officially named the most environmentally-friendly building in the world, featuring the latest sustainable technology.
Today's visit marked the 150th anniversary of the Co-Operative movement, which now employs 95,000 people in the UK.
The Queen was greeted by crowds of well-wishers and slightly bewildered rail passengers when she arrived at Piccadilly station for the start of a visit to Manchester.
Accompanied by the Duke of Edinburgh, she arrived slightly late on the Royal Train at platform one.
The Queen strolled down the 100m long platform to the surprise of some travellers waiting for their train on the opposite platform.
There were cheers as she emerged into the main station concourse.
The Queen, who was wearing a light blue coat and darker blue hat, walked through the station an honour guard of military personnel and British Legion flags, and stopped to talk to the crowd and accept flowers as she made her way to a waiting car outside.
The Queen and The Duke of Edinburgh will travel to Manchester today. The royal couple will take a tour of the Co-op's new eco-friendly headquarters before visiting The Factory Youth Zone in Harpurhey.