The four-time major winner carded a two-over-par 74 at the Ayrshire venue after dropping four shots in his first four holes despite starting out in relatively benign conditions.
The disappointing effort left McIlroy seven shots off the pace, set by one of his playing partners, 2015 winner Rickie Fowler, as well as English duo Ian Poulter and Callum Sinkwin.
McIlroy, making his first appearance in the event since 2014, had spoken on Wednesday about how he’d been working on his wedge game since missing the cut in last week’s Irish Open at Portstewart.
It must have been bitterly disappointing, therefore, that he had a couple of shots in front of big first-day crowd at the Irvine venue that had to rank among the worst of his career.
He found a bunker after coming up short left at the 121-yard 11th to drop a shot before a woeful effort following a majestic drive also cost him a shot at the next.
It then went from bad to worse for the world No 4 as he dumped his approach at the 13th into a burn, semi-duffed his chip and took a double-bogey 6.
To his credit, McIlroy covered the remaining 14 holes in two-under, picking up three of four birdies he made at par-5s.
However, it wasn’t the start he was looking for as he searches for a much-needed confidence boost heading into next week’s Open Championship at Royal Birkdale.
In contrast, Fowler got off to an encouraging start with a flawless five-birdie effort as he matched scores posted earlier by Poulter and Shinkwin.
“I played pretty good,” said the American, who won this event at Gullane two years ago thanks to a wonder shot at the 72nd hole.
“It is a lot of fun to be back at the Scottish Open and it is a great way to get ready for The Open.”
Poulter, who came through one of last week’s final qualifiers to book his Birkdale berth, signed for an eagle and five birdies.
“I’m pretty happy as I hadn’t been hitting the ball well at all on the range the last couple of days,” said the 41-year-old.
Shinkwin, a 23-year-old former English Amateur champion, eagled the last after earlier making five birdies.
Open champion Henrik Stenson’s return to Ayrshire got off to a nightmare start as he found heavy rough with his opening drive of the day at the 10th and ran up a triple-bogey 7.
But, helped by a birdie at the next, the Swede bounced back to salvage a level-par 72.
Scottish No 1 Russell Knox had to settle for a 74, as did David Drysdale while Paul Lawrie could only manage a 77.