Police found the body on the woman's property in Haar in the east of the city after receiving a tip-off three weeks ago.
The victim went missing in 2008 and had been presumed to still be alive, after someone reported sighting him in 2010, the Süddeutsche Zeitung reports.
The woman and her current boyfriend were arrested after police dug the body up in her garden and are currently in custody.
Prosecutors believe the woman murdered her ex-boyfriend in December 2008 and that she acted alone.
They also believe that she took advantage of a moment in which her victim was defenceless to carry out a premeditated murder.
A third man has now also been arrested. The 34-year-old is not alleged to have taken part in the murder but police say he helped to dispose of the body afterwards - as did the the current boyfriend who is currently in custody.
The police believe the man, who was born in 1980, was kept in the woman's house for several months after his murder and was only buried the following summer.