Lisa Michelle Mitchell, 31, was the mother of two young children and was last seen alive at the home in October 2012.
Investigators say they got a search warrant for the Calgary residence on Friday.
An autopsy was planned for Monday.
Allan Shyback, 38, faces charges of second-degree murder and causing an indignity to a body.
He was to appear in court Monday, but the case was rescheduled for Tuesday.
Officers have said the couple had minor, limited domestic history with police, but that no charges were ever laid.
They say Mitchell's children are aged 5 and 7, and that the accused is the father of one of them.