David Gilroy, 49, denies murdering Suzanne Pilley in Thistle Street, Edinburgh, or elsewhere in Scotland, by unknown means on May 4, 2010.
The jury of eight men and seven women began considering their verdict on Tuesday afternoon.
They continued their deliberations throughout yesterday and returned to the High Court in Edinburgh this morning to deliberate again.
Gilroy, from the Silverknowes area of Edinburgh, further denies attempting to defeat the ends of justice between May 4 and May 6, 2010, by concealing 38-year-old Ms Pilley's body and transporting it to various locations in Scotland in the boot of a car.
In his closing speech, Jack Davidson QC, defending Gilroy, said there was no "hard, convincing evidence".
On Monday, the jury heard the prosecution allege Gilroy killed Ms Pilley in the basement of their work building.
Advocate depute Alex Prentice QC said the Crown case is that she was then placed in the boot of his car and driven to a "lonely grave" in Argyll.
The trial, at the High Court in Edinburgh, is in its 19th day.