The couple's lawyer Gernot Lehr issued a statement saying they had physically separated over the weekend, confirming a story in the Bild newspaper that the couple had split.
Bettina Wulff will remain in the family home in a village north of Hannover with their four-year-old son and her son from a previous relationship, the paper said.
It was the purchase of this house that created the first problems for Wullf when he was made president in 2010 - he had failed to declare a sweetheart loan of €500,000 from a regional businessman friend while he was state premier of Lower Saxony.
His reaction to initial reports of the story was ill-advised for the holder of such high office - he made aggressive phone calls to top editors Bild after the paper reported the story. Further revelations of free holidays he and his family enjoyed courtesy of other businessmen eroded any trust and support he had previously enjoyed in the post.
He lasted less than two years before resigning last February, a pasty-faced Bettina by his side as they faced the German media and he said he was stepping down.
Last September Bettina published a book "Beyond Protocol" in which she wrote about trouble in their marriage and what strain her husband's job had put on their relationship.
Now it would seem that these difficulties - and perhaps their airing in public - have led to its conclusion, and the former president has, according to Bild moved out of the family home and into a rented flat in Hannover.