His resignation comes on the same day the firm forecast record quarterly profits, citing higher memory chip prices.
Meanwhile, according to commentators, the surprise resignation of Samsung's chip and display head came amid expectations he would take on bigger roles following Lee's arrest in February and the departures of other key executives in the wake of the bribery scandal.
While expressing concern that the company was "confronted with unprecedented crisis inside out", alluding to the conviction of its leader, Kwon said he hopes his resignation can be a good opportunity for the company to turn things around and make bold attempts at innovation.
Mr Lim said "the current management structure seems to be a complicated web that does not clarify, but rather confuses".
Leadership problems have not hindered the company's business progress, nor have they slowed progress in terms of making major plays in new markets.
The 60 company strong Samsung conglomerate it undoubtedly weathering a severe management crisis.
He was accused of giving KRW 41bn (£29m) of donations to nonprofit organisations run by Choi Soon-sil - a close friend of former president Park - in return for political favours.
However, the leadership troubles do not appear to have hit the company's bottom line yet. He will step down as chief executive and vice chairman of Samsung Electronics in March next year.
Before Kwon's resignation, it projected operating profit had nearly tripled year-on-year in the three months to the end of September to KRW 14.5trn.
His Samsung Electronics stake, albeit below one percent, is now worth 2.3 trillion won ($2.03 billion).
While we'll have to wait to learn the particulars behind those numbers, the company has previously said that Galaxy Note 8 launched with record numbers of pre-orders for the company's phablet range, and that global demand for memory remains high and means the company enjoys fat margins.
He will miss another record earnings announcement expected in the fourth quarter as he is expected to stay in prison at least until February, when the appellate court hearing his case is likely to try to rule on the bribery suit.
"[Samsung] has been showing record performances", Kwon said.
"It may be felt that someone new can drive greater innovation and manage the firms move into new areas as the smartphone market matures", he said.