The Saudi journalist was at the consulate in order to obtain documents that certified his divorce.
His Turkish fiancé was waiting outside for 11 hours when she reached out to an advisor to the Turkish President as per Mr Khashoggi’s request.
Now Turkish authorities are saying there is evidence to suggest the journalist never left the building and was murdered there.
Officials have said “the murder was premeditated and the body was subsequently moved out of the consulate”.
Turkish police also believe the Saudi dissident was killed by a team of assassins “especially sent to Istanbul and who left the same day”.
Turan Kislakci, the head of the Turkish Arab Media Association and a friend of Mr Khashoggi’s, said that Turkish officials had called him to confirm his friend’s death.
Mr Kislakci said: “They confirmed two things: He was killed and his body was dismembered.”
Saudi Arabia was quick to dismiss any accusations of foul play.
Crown Prince Mohammad Bin Salman said that Turkish authorities were free to search the premises for the missing journalist and insisted that Saudi Arabia has “nothing to hide”.
On Friday, the Crown Prince confirmed that Mr Khashoggi’s visit was very brief.
He said that, according to his understanding, Mr Khashoggi had left the consulate within an hour of entering.
Mr bin Salman added that the Foreign Ministry was working to “see exactly what happened at that time”.
Turkish President Recep Tayyip Erdogan said on Sunday that he was personally following the case and that the investigators were looking at all the camera records and monitoring airports.
He added that he was hopeful for a positive outcome.
Mr Khashoggi’s fiancé, Hatice Cengiz, was also hopeful.
Ms Cengiz took to Twitter to say that she “did not believe he has been killed” and that she was waiting for official confirmation.
Mr Khashoggi fled his native Saudi Arabia in 2017 amid a clampdown on opposing views of the Saudi regime.
He later took up a position as a columnist with the Washington Post where he would regularly take aim at Saudi Arabia’s conduct in Yemen’s civil war as well as the policies of the Crown Prince.