Mr Emery, who will take the post for a two-year period, is currently chairman of the Scottish Police Authority.
In the past he has been chairman of Scottish Enterprise in Glasgow and managing director of BAE Systems Surface Fleet Solutions, where he was in charge of shipbuilding on the Clyde and support services at Portsmouth.
Mr Emery replaces Varry McMenemy, the managing director of call centre business Bellcom Worldwide.
Deputy president for the next two years is lawyer Neil Amner who is a partner and head of construction and infrastructure at DWF. At the Chamber's annual general meeting last night Nigel Kirby, Siemens account director for Scotland, and Suzanne Burns, STV's human resources and communications director, joined the management board.
In addition, during the meeting IBM's Gillian Docherty, Richard Brown from Glasgow City Council and Neal Juster from Glasgow University were elected to the ruling council of the Chamber. Mr Emery said: "I am very pleased to become Chamber president, and impressed by the additions to our board and ruling council. They join us at a time of major development for the Chamber, where we will focus on increasing our influence as a delivery and policy partner in championing Glasgow and achieving the aims and objectives of the city's economic strategy."
Mr Emery said his duties would include making sure the Chamber is campaigning on policy issues, offering training opportunities, advising on exports and ensuring a programme of relevant events for members.
Glasgow Chamber chief executive Stuart Patrick said he was looking forward to working with the "highly experienced pairing" of Mr Emery and Mr Amner over the next two years.