2008- Present : Kolkata Knight Riders & Retirement -

In February 2008, Ganguly joined as the captain of Kolkata Knight Riders (KKR) team, owned by Bollywood actor Shahrukh Khan. On 18 April 2008, Ganguly led the KKR, in the IPL Twenty20cricket match. They had a 140 run victory over Bangalore Royal Challengers captained by Rahul Dravid and owned by Vijay Mallya. Ganguly opened the innings with Brendan McCullum and scored 10 runs while McCullum remained unbeaten, scoring 158 runs in 73 balls. On 1 May, in a game between the Knight Riders and the Rajasthan Royals, Ganguly made his second T20 half century, scoring 51 runs off of 39 balls at a strike rate of 130.76. In his innings, Ganguly hit four 4s and two sixes, topping the scorers list for the Knight Riders.

On 7 July 2008, media reported that Ganguly was being projected as a candidate for the post of President of the Cricket Association of Bengal (CAB) against his former mentor Jagmohan Dalmiya. Reports also suggested that he could run for the post of BCCI President in 2014 as East Zone's representative. Ganguly himself did not deny the reports and did not rule out any such move. The same year in October, Ganguly announced that the Test series against Australia starting in October 2008 would be his last and stated "[t]o be honest, I didn't expect to be picked for this series. Before coming here, [at the conference] I spoke to my team-mates and hopefully I will go out with a winning knock." Ganguly played in every game of the four-Test series and amassed 324 runs at an average of 54.00. While playing the second Test match of the series in Mohali, Ganguly scored his final test century. In the Fourth and final Test, with India needing one wicket to secure a victory, the Indian captain, Mahendra Singh Dhoni, invited Ganguly to lead the side in the field for the final time. India regained the Border-Gavaskar Trophy, winning the series 2–0.

In May 2009, Ganguly was removed from the captaincy of the KKR for IPL 2009, and was replaced by McCullum. The decision was questioned by media and other players of the team, when KKR finished at the bottom of the ranking table with three wins and ten losses. After that, television channel Zee Bangla appointed him as the host of the reality quiz show titled Dadagiri. It presented participants from the 19 districts of West Bengal, who had to answer questions posed by Ganguly. By August, he was appointed the chairman of CAB's Cricket Development Committee. The job of the committee is to receive a report from the selectors at the end of every cricket season, assess the accountability of the selectors and make necessary recommendations. He played for the Ranji cup in the Bengal team in October 2009. Ganguly scored 110 in the match against Delhi team, and was involved in a partnership of 222 runs with Wriddhiman Saha.

In the third season of Indian Premier League, Ganguly was once again given the captaincy of Kolkata Knight Riders, after the team ended at the bottom in season 2. The coach John Buchanan was also replaced by new coach Dav Whatmore.