The 25-year-old man from the Brisbane suburb of Flagstone was arrested at Melbourne Airport on Saturday after travelling to Melbourne.
He was interviewed by police and subsequently charged with the murder of 28-year-old Sergio Cuesta, who went missing in September.
Mr Cuesta was last seen when he was dropped by a friend at a Jabiru Drive address in Chelsea Heights, 30km southeast of Melbourne.
He had earlier been at a birthday dinner in the CBD, on the night of September 16.
A concerned female friend, who was also at the dinner, alerted authorities after failing to hear from him for five days.
The Flagstone man was remanded in custody and will face Melbourne Magistrates Court on Monday.
A 25-year-old Logan Reserve man and 23-year-old Flagstone woman were also arrested in Brisbane on Saturday with the help of Queensland police.
They are expected to face an extradition hearing in a Brisbane court on Monday.
Properties in Flagstone and Logan Reserve were raided but police have not revealed if any items were seized.
Michael Jeffrey Frankland, 49 from Mt Eliza, last week became the first person charged with Cuestas's murder.
Another man, a 48-year-old from Cranbourne, was also arrested but released without charge.
Six firearms, a pill press, various quantities of what appear to be dried cannabis and cocaine, cannabis plants, a crossbow and a Taser were seized from a Mt Eliza property.
After initial inquiries by local police, Cuesta's disappearance was deemed suspicious and the missing persons squad took over the investigation.
Prior to his disappearance, he had been living in an apartment on Queens Road in Melbourne and was subject to an expired student visa.
He was also on bail in relation to drug offences and was known to have contact with people suspected to be involved in trafficking.
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