Three successive bogeys from the third had left the Masters champion and last week’s Irish Open winner two shots outside the projected two-under mark required to progress to the final two rounds at Wentworth.
A birdie at the eighth, his first in 10 holes, started him heading back in the right direction and four in five holes immediately after the turn moved him to five under and far more comfortable.
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However, having carved his drive out of bounds at the last he finished with a double-bogey seven.
McIlroy has played the par-fives particularly poorly this week and is four-over for his last five but his level-par round of 72 left him three under for the tournament, level with playing partner Shane Lowry who carded a two-over 72.
A mixed round for Lowry started poorly with a bogey on the first. He regained that shot on the fourth but bogeys on seven and nine saw him turn in 37.
The Offalyman looked to be getting things back on track with a birdie on 10 before dropped shots on 14 and 15 were followed by a brace of birdies on the way home. However, a sixth bogey of the day on the par-five last saw him sign for a 74.
Both Irishmen are eight shots behind Ryder Cup team-mate Viktor Hovland after his 66.
Hovland, who eagled the 18th for the second day running in addition to four birdies, was the clubhouse leader on 11 under.
“I can’t remember the last time I’ve chipped it and putted it as well as I have the last couple of days,” he told Sky Sports.
“I’m super-happy to be where I am at. Scoring-wise it is incredible as as I am really struggling off the tee and trying not to hit it off line and into the trees and so far it’s been good and from there I’ve been amazing.
“But I do want to play the game a little more stress-free.”
Viktor Hovland set the clubhouse lead at Wentworth (Adam Davy/PA)
Spain’s Pablo Larrazabal is the Norwegian’s closest challenger in the clubhouse on 10 under after a 67, while Ryder Cup vice-captain Alex Noren is in a share of third a shot further back after a 68, alongside Scotland’s Richie Ramsay who carded a 69.
Of the other members of Luke Donald’s European team to complete their second rounds Tyrrell Hatton was at five under and Jon Rahm three under, benefiting from a huge stroke of luck when his drive at the 18th was prevented from going out of bounds after landing in a buggy parked in the left rough – from where he made birdie.
Scotland’s Bob MacIntrye is right on the cut line at two under after a second successive 71 but Donald himself looks like playing no further part after a 71 left him one under.
Ryder Cup rookie Rasmus Hojgaard will not have received much of a confidence boost from his performance at Wentworth, however, as a 75 saw him finish five over.