Last month it was reported that Clifton was to be made redundant by the broadcaster as the BBC Journalism group was closed.
Today MSN UK announced Clifton would be joining the company in a role previously held by Peter Bale, who is leaving his current job as international programming director for a newly created digital role at CNN.
Clifton will lead an editorial team of 50 and oversee all content on the MSN platform, reporting to former BBC head of future media and technology, Ashley Highfield, who is UK managing director of Microsoft Consumer and Online.
"I am delighted to welcome such a great talent as Pete in to Microsoft," Highfield says in the release.
"His many years as a senior member of the BBC News team, sitting on the journalist board, and in particular the four in which he was Editor-in-Chief of BBC News Online where he was responsible for over 400 staff, speak volumes about the enormous contribution and impact he will deliver to our MSN business in the UK."
"I've always had great respect for Microsoft and, in particular, MSN, which I believe is well-positioned to capitalise on the dramatic changes taking place in the world of media today," Clifton added in the release.
MSN UK has also appointed the Telegraph's online news editor Duncan Hooper as managing editor for news and sport, the announcement adds.
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