After the second session, the No. 16 Racing for Holland Dome had all of its lap times deleted due to a fuel infringement caused by possibly its fuel tank not being extensively cleaned. Teams running with more powerful engines for qualifying stopped utilising them and installed the power units they would use for the race in order to comply with an ACO regulation that forbade teams changing engines before the final qualifying session and the race. The 13 June's first qualifying session had Capello improve provisional pole position with a 3 minutes and 29.905 seconds lap that he set late in the session and broke the overall lap record held by Martin Brundle in a Toyota GT-One since the 1999 race. He was followed by Kristensen's No. 2 Audi in second after the latter was delayed by a slower car and Sarrazin's third-placed No. 14 Team Oreca Dallara though he aborted his first timed lap due to traffic. The No. 3 Audi remained in fourth place, and Blundell's No. 27 MG-Lola maintained fifth though his engine failed at the first chicane on the Mulsanne Straight. Dalmas' session was ended early with an electrical failure that caused him to abandon his Audi at the side of the track. Although it stopped on its first lap with a transmission fault, the Prodrive Ferrari continued to lead the LMGTS category, and The Racer's Group Porsche maintained the LMGT class lead despite Luhr making a driver error that put the car into the gravel trap at the Dunlop Chicane, and a broken water sealant when Kevin Buckler was driving the vehicle. The session was stopped halfway through for ten minutes to allow marshals to dry a large amount of spilled oil at the Ford Chicanes.