But McIlroy bounced back at the eighth, his birdie putt dropping in the front of the cup, and he gained his third shot of the round on the par-five 12th with a tidy up-and-down.
A wonderfully judged approach from the rough at 13 set up another birdie chance for the 2016 champion but his putt slid by on the right and his frustrations deepened with back-to-back bogeys on 14 and 15 dropping him back to level par.
But as the sun faded and the temperature dropped, McIlroy delighted the fans by closing with three birdies to strengthen hopes of his first professional win on Northern Irish soil.
But while McIlroy left himself in a strong position, his playing partner and fellow countryman Tom McKibbin has work to do after an opening 74.
McKibbin, who started with a bogey after finding trouble with his opening drive, dropped to five over after a double at 16 but matched McIlroy’s birdies at 17 and 18 to sit eight shots adrift.
Lowry, too, has work to do but a birdie on the last leaves the 2019 Open champion just six back, his 72 a satisfactory return after a couple of early bogeys.
Among the group at two-under are England’s Dan Brown, who contended at the Open at Troon in July, and veteran Dane Soren Kjeldsen, the 2015 Irish Open champion at Royal County Down.