Brian Jarrard, Bungie's director of franchise and community affairs, told BBC News that the move had not come about because of any pressure to keep doing Halo titles.
"Microsoft has always been flexible and they certainly have not had any gun to our head for more Halo titles.
"We're committed to doing a Halo project with Peter Jackson (Lord of the Rings director)."
He said the company had at least one other title that was close to being greenlit by Microsoft that "may or may not be Halo related".
"We are not walking away from Halo," he added.
Harold Ryan, studio head at Bungie, said Microsoft's platforms would remain the firm's "primary focus" but the move opens up the possibility of the studio developing for other consoles.
"Bungie is like a shark. We have to keep moving to survive," said Jason Jones, Bungie founder and partner.
'Independent roots'
Shane Kim, corporate vice president of Microsoft Game Studios, said the company was "supporting Bungie's desire to return to its independent roots".
He said Microsoft would to invest in Halo entertainment property with Bungie and other partners, such as Peter Jackson, on "a new interactive series set in the Halo universe".
"We look forward to great success with Bungie as our long-term relationship continues to evolve through Halo-related titles and new IP created by Bungie," he added.
Bungie was formed in 1991 and produced ground-breaking titles Marathon and Myth. The company was bought by Microsoft soon after it began work on the first Halo game.
Mr Jarrard said everyone in the Bungie team had been offered the chance to stay with Microsoft.
"Except for one or two people for personal reasons, everyone opted to work with Bungie," he said.
On the Bungie website, Frank O'Connor, lead writer on Halo, explained the move to the community of fans: "Bungie has long been built on creativity, originality and the freedom to pursue ideas.
"Microsoft agreed, and rather than stifle our imagination, they decided it was in both our best interests to unleash it."
