Yoon is on trial for attempting to carry out a coup, after his failed declaration of martial law in early December.
The 64-year-old Yoon attended the court himself on Thursday, when the main trial began with the first interrogations.
He is the country's first sitting president to be brought to trial in a criminal case. He denies any wrongdoing and has called the martial law declaration legitimate.
His lawyers have insisted that the investigation against him has lacked grounds from the start. They claim that it was within his powers as head of state to declare martial law.
Yoon has been imprisoned since he was arrested in a large police operation on January 15, after refusing to appear before investigators and instead barricading himself in the presidential palace.
Yoon also appeared in another court on Thursday. Parallel to the criminal case, an impeachment trial is also underway, where the country's Constitutional Court will decide whether Yoon should be formally removed from office.
His presidential powers were suspended when he was impeached on December 14, but if Yoon is removed from office, the country must hold new presidential elections within 60 days.
South Korea's President Yoon Suk-Yeol introduced martial law on the evening of December 3, according to himself to protect the country from "communist forces". This was done with reference to the opposition having paralyzed the government's work.
The night of December 4, the parliament voted to repeal the martial law and the state of emergency was declared invalid.
Yoon Suk-Yeol was stripped of presidential power on December 14, when the parliament voted to bring him to trial.
In addition to the impeachment process in the Constitutional Court, the anti-corruption unit and the police have conducted a joint criminal investigation against Yoon.
