Joshua Searston, 27, and Dewald De Klerk, 30, have pleaded not guilty to murdering Andrew Walsh, 35, in November 2021 at their Brisbane Supreme Court trial.
Mr Walsh's body was found at the bottom of an oil pit at a Coopers Plains transport depot in Brisbane's south in February 2022, the court was told.
Mr Walsh - known as "Ghost" - was discovered more than a month after he was reported missing by his mother.
Detective Senior Sergeant Jason Kitto was shown pictures of the transport depot in court on Tuesday, detailing how police were able to find Mr Walsh's body.
Police removed a grate covering a pit in the depot's warehouse that had previously been covered by a car on February 19, 2022, the court was told.
"When we took that lid off it looked like there was a layer of fresh oil over the top," Det Kitto told the court.
"So we decided due to the fresh concrete dust and the splatter around the back ... that would be an area of interest to us."
Contractors dug deep holes into the pit to gauge depth and confirmed it was new concrete, the jury heard.
"I couldn't understand why there would be a pit that was only 30cm deep with oil on top," Det Kitto said.
Further drilling hit timber then came a smell, the court was told.
"They continued to dig deeper and the smell came out of the hole?," crown prosecutor Chris Cook asked.
"Correct," Det Kitto said.
Asked if flies came into the area as a result, Det Kitto said: "Correct".
After five hours of digging found wooden pallets and car batteries within the concrete, police saw the outline of something wrapped in plastic, the court heard.
An image of a forensic officer delicately cutting through the plastic was shown to the court.
Bones were found, the jury heard.
Det Kitto said Mr Walsh's body was located 2.5m into the pit and "strapped to a toilet system".
It took days to remove the body, he said.
The body was found with significant decomposition, nasal bone fracturing, dislodged teeth, fracturing around the right shoulder blade and collarbone along with abdomen stab wounds, the court was told on Monday.
Prosecutors allege Mr Walsh was killed on or about November 7-8, 2021.
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