O'Connell suffered a recurrence of his back injury in October 2012 and had to undergo surgery on New Year's Eve, which ruled him out of rugby until early April 2013. However, O'Connell returned early from the injury, having made a quicker-than-expected recovery, and played 40 minutes for Munster A on 12 March 2013. Having come through a full 80 minutes for Young Munster, O'Connell then lined out for the senior Munster side in their league fixture against Connacht on 23 March 2013, again playing the full 80 minutes. He captained Munster in the absence of Doug Howlett in the 12–18 Heineken Cup quarter-final victory over Harlequins on 7 April 2013, a game in which he won the Man-of-the-Match award. He also captained Munster in the 16–10 semi-final defeat to ASM Clermont Auvergne on 27 April 2013.