Police deemed the disappearance of Jayden Stewart Selfe suspicious and launched an intensive search of a bush area and a residential property in Perth for clues.
A 42-year-old man from Banksia Grove, a 40-year-old man from Attadale and a 39-year-old woman also from Attadale have been charged with murder.
They have been remanded in custody to appear before Perth Magistrates Court on Monday.
The search areas in recent days included bushland northeast of Wanneroo and a residential property on Money Road in Attadale, a riverside suburb of Perth.
Police last week said they had "grave concerns" for Mr Selfe's welfare and believed his last known contact with people known to him was in May 2025.
WA Police Commissioner Col Blanch told reporters last week police feared Mr Selfe was dead.
"I don't want to rule out that he may be alive but certainly the information we have would suggest that harm may have come to Mr Selfe," he said.
Detectives received information in August which led them to deem Mr Selfe's disappearance suspicious.
Detective Acting Senior Sergeant Leigh McKnight told reporters on Tuesday police were investigating whether Mr Selfe had been killed before being dumped in Wanneroo bushland.
During four days of searching a number of items were located and identified that were of "significant interest" to the investigation.
"From ongoing forensic examinations, and information we have from a number of witnesses, there's nothing that leads us to believe he's still alive at this point in time," he said.
Sen Sgt McKnight thanked people who had come forward and provided police with relevant information to the case.
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