The 49-year-old from Mt Eliza will appear in Melbourne Magistrates court on Wednesday charged over the disappearance of 28-year-old Sergio Cuesta last September.
Mr Cuesta was last seen when 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.
Police arrested two men on Tuesday over his disappearance.
A 48-year-old Cranbourne man was released without charge.
But on Wednesday afternoon the missing persons squad charged the Mt Eliza man with murder.
Three firearms, a pill press, various quantities of what appear to be dried cannabis and cocaine, cannabis plants, a crossbow and a conducted energy device were seized from a Mt Eliza property.
After initial inquiries by local police, Mr 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 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.
Detectives remain keen to speak to anyone with information about his movements in the lead up to his disappearance.
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