As part of the deal, Ampersand is to create a new visitors café and will run the public bar and restaurant, as well as all daytime events.
The firm will also be one of the approved caterers for evening events.
The appointment follows the news that the museum will be the base for the German National Olympic Committee for the Olympic and Paralympics Games in 2012.
"We are delighted to be embarking on this exciting new partnership with Ampersand," said Museum of London Docklands head of hospitality Elizabeth James.
"We were impressed by its dynamic approach to refreshing the menus at the visitor café, public bar and restaurant, and we are looking forward to welcoming guests to these exciting new spaces."
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