Joshua Searston, 27, and Dewald De Klerk, 30, have pleaded not guilty in Queensland Supreme Court to murdering Andrew Walsh, 35, at a transport business in Brisbane's south in November 2021.
The body of Mr Walsh - known as "Ghost" - was not discovered until March 2022 when police dug down 1.5 metres at the Coopers Plains transport depot.
De Klerk pleaded guilty to interfering with a corpse at the start of the trial.
The jury started deliberating on Tuesday afternoon after hearing evidence and closing statements over eight days in the trial.
Chief Justice Helen Bowskill told the jury in her summation on Tuesday that they had heard "confronting details" about Mr Walsh's death and how the police uncovered his body.
She instructed the jury not to hold prejudice against Searston and De Klerk because of those details.
"The defendants do not have to prove their innocence. They do not have to prove any facts," she said.
Justice Bowskill told the jury they would have to decide whether the witnesses, some of whom were accused of other criminal offences, had given honest and credible evidence.
"You don't have to determine if they are the kind of people you would trust to look after your children," she said.
Crown prosecutor Chris Cook last week told the jury in Brisbane the defendants attacked and stabbed Mr Walsh believing he had been "franking", which meant sexually assaulting someone after drugging them.
"De Klerk assisted Searston's plan to do serious harm to Mr Walsh ... there's a perfect storm brewing that night," Mr Cook said in his closing submissions.
De Klerk's barrister David Funch previously told the jury a major witness for the prosecution, Jessica Noy, had been "disgracefully dishonest" while giving evidence and could not link his client to causing Mr Walsh's death.
Searston's barrister Anna Cappellano previously said her client did not dispute having a physical confrontation with Mr Walsh.
"The main issues are what did (Searston) do and what did he intend to do on that night as it relates to Mr Walsh," Ms Cappellano said.
Justice Bowskill instructed the jury to reconvene on Wednesday morning after they did not deliver a verdict after a few hours of deliberation.
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