The contentious bidding process for the contract pitted Microsoft, Amazon, and Oracle, among others, against one another.
The resulting system will store and process vast amounts of classified data, allowing the U.S. military to use artificial intelligence to speed up its war planning and fighting capabilities.
The Department of Defense emphasized in an announcement that the process was fair and followed procurement guidelines.
Over the last year, Microsoft has positioned itself as a friend to the U.S. military. President Brad Smith wrote last fall that Microsoft has long supplied technology to the military and would continue to do so, despite pushback from employees.
Microsoft, Amazon, Google and other tech giants have faced criticism from their own employees about doing business with the government, especially on military and immigration-related projects.
Microsoft and Amazon did not immediately respond to a request for comment.