The company opened the first of its modern retail stores in 2009, around the time of the launch of Windows 7.
According to its website, Microsoft has 83 stores worldwide, including 72 stores in the U.S., and several others abroad where it showcases and sells laptops and other hardware.
Friday's announcement reflects what the company calls a "strategic change" for its retail business as sales increasingly shift online.
Microsoft will keep four of its stores open, in London, New York, Sydney and its home base of Redmond near Seattle. But they will be "reimagined", the company said in a statement.
All employees will have the opportunity to remain with the company, Microsoft said.
Microsoft Corp. said the closures would result in a pretax charge of about $450 million, or 5 cents per share, taken in the current quarter ending June 30.