Former world number one McIlroy shot a stunning course-record 64 in his first round at Royal Aberdeen, but that must have seemed a distant memory as he followed it up with a seven-over par 78.
McIlroy, aiming for a morale-boosting win ahead of next week's Open Championship at Hoylake, therefore found himself six shots off the lead at level par, after a disappointing day that included a seven at the 12th.
Argentine Gonzalez held a two-shot advantage when he teed off on the 18th, but a double bogey ensured he slipped back to six under alongside Kristoffer Broberg and home hope Marc Warren.
Gonzalez, seeking a first European Tour win since 2009, birdied three of the first five holes on Friday.
However, he found rough from the tee on the last and was then forced to take a drop after firing across the fairway into a bush.
The day could have been so much better for Sweden's Broberg, who double bogeyed the 14th and also gave up ground at the final hole.
He and Gonzalez had to settle for rounds of 71, while Warren claimed birdies at 16 and 18 to complete a 69 that enhances his chances of pulling off a popular victory on home soil.
Justin Rose moved up to fourth on the leaderboard with a 68, which leaves the Englishman just a shot adrift of the leading trio, while Rafael Cabrera-Bello and Mikko Ilonen matched that mark to climb into the top 10.
Rose revealed he had found it difficult to get to grips with the course on Thursday, and is thrilled to be in contention at the halfway mark.
He said: "I was a couple over yesterday early in my round and everybody else seemed to be going low and I was finding the course really, really difficult and wasn't really comfortable with my game. So where I've got to after 36 holes I'm delighted."
Defending champion Phil Mickelson suffered a frustrating Friday as he went round in 73 to be one under overall.