Cory Breton, 28, and Iuliana Triscaru, 31, were killed at Kingston in Logan, south of Brisbane, on January 24, 2016.
Police divers found their bodies two weeks later locked in the toolbox submerged in Scrubby Creek.
The jury on Friday returned its verdict after deliberating since 10.45am on Wednesday.
The trio are set to be sentenced at a later date.
None of the accused elected to testify in their own defence.
The jury previously heard evidence that the victims could have been alive when the toolbox was thrown into the water and weighed down with concrete.
Crown prosecutor Nathan Crane previously told the jury he would allege Daniels and Taiao were liable for murder by forcing the victims into the toolbox at a Kingston unit in the hours before their deaths.
Thrupp either threw the toolbox into nearby Scrubby Creek or was present when it happened, Crane said.
Thrupp’s defence barrister Jessica Goldie previously said other men, including Taiao or a prosecution witness, could have been a passenger in a utility vehicle that took the toolbox containing Breton and Triscaru to Scrubby Creek, rather than her client.
Goldie said a claim by a witness that her client confessed to him he shot Breton and Triscaru in the head was a “complete fabrication” and was contradicted by forensic evidence.
Taiao’s defence barrister Lars Falcongreen told the jury a “star witness” for the prosecution had given evidence that showed his client had no knowledge of any plan to kill.
Daniels’ defence barrister John Fraser said his client had taken part in what he thought was a “boot ride”, which was a common punishment in drug-dealing circles involving detaining people to scare them.
The trio faced a retrial this month after the Court of Appeal in July 2024 set aside murder convictions for Thrupp, Taiao and Daniels and ordered that they receive new trials.
In 2021, Thrupp, Taiao and Daniels were each found guilty of two counts of murder.
The 2024 Court of Appeal decision ruled there had been a miscarriage of justice on grounds including how the jury was directed in relation to the offences of murder.
However, the trio’s appeal against torture charges, relating to their assaults on Breton and Triscaru, was dismissed.
