The news was confirmed on Friday evening by the Offical Donegal GAA Twitter account.
He's stepped down after four years in charge of the county's footballers, a reign which saw his side win the 2012 All Ireland title.
McGuinness' last game in charge was last month's All Ireland final defeat to Kerry.
It's understood that Jim McGuinness had earlier informed players of his decision to leave the post.
Jim McGuinness steps down as Manager of the Donegal Senior Football Team: Statement Attached. pic.twitter.com/xrCN1AwDgk
— Official Donegal GAA (@officialdonegal) October 3, 2014