The 2008–09 season marked a shift in focus for O'Driscoll. While retaining the Irish captaincy under new coach Declan Kidney, he handed the honour of Leinster captain to Leo Cullen. O'Driscoll scored two tries in the defeat of English champions London Wasps, however this victory was followed by away defeats for Leinster to both London Wasps and Castres. Leinster advanced to the quarter-finals to face Harlequins at the Twickenham Stoop. When O'Driscoll was absent through injury in April 2009, Leinster relinquished their Magners League crown to Munster at Thomond Park. Against Harlequins, Leinster scored a 6–5 victory, the game infamous for the Bloodgate incident.
In the semi-final against rivals Munster in Croke Park, an 82,206 sell out, O'Driscoll was awarded the man of the match award (which he later dedicated to the entire team) after an intercept try completed a convincing win for Leinster and sent O'Driscoll to his first Heineken Cup final. Leinster captured the Heineken Cup against Leicester Tigers on 23 May 2009. The 19–16 Heineken Cup victory included a drop goal from O'Driscoll who was suffering from a shoulder injury.
In 2009, O'Driscoll was again selected as captain, leading Ireland to win the Triple Crown, Six Nations Championship and their first Grand Slam in 61 years. He scored a try in every match except one, culminating in a 17–15 victory in Cardiff in which O'Driscoll again scored a try and was the RBS man of the match. On 27 March 2009, he was named as player of the 2009 Six Nations Championship, winning the fans' online poll. In May 2009, he was named the Bord Gáis Energy IRUPA Players' Player of the Year for the past season.
On 15 November 2009, in a 20–20 draw against Australia at Croke Park, O'Driscoll scored a last minute try. The next day, he was named as one of the seven nominations for the 2009 International Rugby Board player of the year, but controversially missed out to Richie McCaw for this title by a solitary point.
On 21 April 2009, O'Driscoll was selected as part of the 2009 British & Irish Lions tour to South Africa. On 1 June 2009, he was named as captain of the Lions for the game against the Golden Lions taking place on 3 June, in place of the rested Paul O'Connell. He was also named in the outside centre position for the Lions in their first test of the 2009 tour against South Africa, in which he made two assists as the Lions lost 26 – 21. He was forced to withdraw from the tour on 30 June before the third and final test due to a head injury and subsequent concussion he suffered in the second test.