The reigning Masters champion found the water four times on a tough day as he made only two birdies, following on from his fine first-round 66 on Thursday.
McIlroy, 36, is targeting his eighth professional title in Dubai after four Dubai Desert Classic victories and three wins in the European Tour's Tour Championship.
But now with the Northern Irishman on two-under at the halfway point, Republic of Ireland's Shane Lowry and Spaniard Nacho Elvira sit joint-first, three shots ahead of him.
The duo both posted rounds of 68 - the lowest of the day - to surge into the lead, with Spain's David Puig and England's Marcus Armitage two shots back in joint-second.
"Very happy. It was hard. It was tricky," Lowry said.
"If I play golf like that for the rest of the season in that frame of mind, I'll be pretty good."
On a windy day at Dubai Creek, eagles were at a premium, however, American Ryggs Johnston overcame the conditions to sink a hole-in-one at the 218-yard par three eighth hole.