The deal, understood to be just weeks from completion, will see Mr Chowdery's fast-growing Property Route business take charge of the mall and seven-storey office block.
A new hotel and casino are planned for the 25,000 sq ft centre, after a makeover intended to bring back shoppers. Current tenants include Greggs, Subway and Ladbrokes.
The refurbishment will be linked to wider plans to revive Altrincham town centre.
Nabeel Chowdery was a pupil at Altrincham's North Cesstrian Grammar School and his £150m Property Route business is now based in the town.
The Grafton centre's price has not be disclosed but is understood to be between £10m and £15m.
The Altrincham buy follows a series of sales and purchases by the Property Route empire.
Earlier this year the firm sold its interests in 2 St John Street, Manchester, for a sum understood to be close to £3.5m.
The Grafton centre is the second major purchase in Altrincham for Property Route. In February 2007 the company purchased Ashley House. The 16,800 sq ft block is now host to the company's headquarters as well as to local businesses.
The block was acquired from solicitors Irwin Mitchell.
Nabeel Chowdery's Property Route has followed in the footsteps of MCR Property, the business founded by older brother Aneel Mussarat.
Last week MCR Property was awarded planning consent for a £27m residential scheme on Queensway in Rochdale. Situated on a six-acre site, the scheme will comprise 141 units, including 31 townhouses.
The ambitious Manchester based property company has also started construction of its scheme in Harpurhey at the former Gala Bingo hall on Rochdale Road which is to provide 46 new residential units with an end value of £8m.
A further 72 units are planned nearby on a site previously home to the Golden Lion pub. In addition work has commenced on the construction of 194 dwellings on Hathersage Road, adjacent to the Victoria Baths.
Mark Hayes, of MCR Property Group, said: "We are pleased to have been able to start the year with the construction of these two new developments, which will boost our existing residential portfolio."
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