Lisa Michelle Mitchell, 31, was last seen alive at the home in October 2012.
Police say her family reported her missing the following month to RCMP in Turner Valley, southwest of Calgary, when they became concerned that they hadn't heard from her for an unusual amount of time.
Investigators say they got a search warrant for the Calgary home on Friday, where the 38-year-old suspect and two young children were still living.
Allan Shyback faces charges of second degree murder and indignity to a body and will appear in court on Monday to face the allegations.
The children, who police say are 5 and 7, were not home at the time of the arrest.
"They are being taken care of at this time, but obviously they are going to need some additional resources later on," said Sgt. John Hebert with the missing persons unit.
Forensics investigators remained at the scene on Saturday. An autopsy has been scheduled for Monday.
RCMP turned the investigation over to Calgary police in January 2013.
Hebert said Mitchell's mother has been notified.
"I think she took the news with a measure of grace considering what the news was," Hebert said.