Yoon, 64, appeared noticeably slimmer, with his hair greyer and cropped short after spending more than two months in prison out of public view and having refused to attend trial since early July on health grounds.
"Survival itself is difficult," Yoon told the court on Friday in a reference to the small solitary cell where he was held, the Yonhap news agency said.
The fresh charges against the conservative former president stem from attempts to block investigators trying to arrest him in January after parliament's impeachment suspended his powers and he barricaded himself in the presidential compound.
The new charges were brought by a special prosecutor appointed in June whose team has widened the investigation of Yoon and several former government and military officials.
At the trial, Yoon's lawyers said the charges were legally unjustified, because the arrest warrant was secured by investigators who lacked legal authority to investigate his actions within the scope of his presidential power.
Seeking his release on bail, Yoon's lawyers called his detention unfounded because he did not pose a flight risk.
It also impaired his ability to mount a proper defence against what the lawyers called a "witch hunt".
The unrelenting pace and intensity of the trial and continued investigation have aggravated complications from pre-existing illnesses, the lawyers said.
Yoon, stripped of office by the Constitutional Court in April, is also being investigated by another special prosecutor who has indicted his wife for corruption.
Yoon has denied all wrongdoing and said it was within his powers as president to declare martial law in December.
He has rejected all investigations against him as politically motivated.
If convicted on the new indictment, Yoon faces more than three years in jail. If found guilty on the insurrection charges, he would face the death penalty or life in prison.
