The EU said last month that it had set 19 October as a provisional deadline for giving its verdict on the acquisition.
When the deal was announced, GitHub had about 28 million developers working on 80 million repositories.
There has been mixed reaction to the acquisition, with open-source developers wary of the Redmond-based software giant's motives in buying GitHub.
One security researcher, Mustafa Al-Bassam, raised the possibility that the NSA could now gain access to the code of GitHub as Microsoft has, in the past, allowed the spy agency access to its systems.
The last big Microsoft acquisition approved by the EU was the purchase of LinkedIn for US$26 billion.