Detectives from the Missing Persons Squad arrested the 53-year-old Melbourne man at 7.20am on Wednesday.
Ms Ristevski went missing from her Oakley Drive, Avondale Heights home on the morning of June 29 in 2016.
Her remains were discovered in the Mount Macedon Regional Park eight months later, on February 20.
During an appearance at the Melbourne Magistrates Court on Wednesday morning, Borce Ristevski entered a plea of not guilty.
"He will be pleading not guilty," his lawyer Rob Stary told magistrate Angela Bolger.
Mr Stary said his client had already been under investigation for a number of months.
"This man doesn't have any history and we want the matter expedited," he told the court.
Ristevski has been remanded in custody and is scheduled to return to court on April 18.
Prosecutor Andrew Tinney SC said police needed extra time to complete their brief of evidence "because of the nature of the investigation and the ongoing work that needs to be a done".
No one from his family was in court.
Karen Ristevski's brother has released a statement thanking police for their work over the last 18 months.
"Today has been a surprisingly emotional day - one which I have been patiently waiting for," the statement read.
"It is in no way a celebration, it's another stage in bringing my beautiful sister Karen the justice she so deserves.
"Again, a huge thank you to the Missing Persons Squad - also to Emily, Lachlan, my cousins and work colleagues who have been very supportive through these long last 18 months."
In March, hundreds of mourners dressed in black filled St John's Uniting Church in Essendon for a private funeral service before Ms Ristevski's body was taken to her final resting place. Borce Ristevski was one of the six pallbearers who carried her coffin during the procession.
