The defeat piled yet more pressure on the shoulders of current boss Ian Brightwell, who is the eighth incumbent in the Macclesfield hot-seat since the departure of McIlroy.
Morecambe nearly took an early lead in the third minute when Macc keeper Jon Brain dropped the ball under pressure from Carl Baker only for Stewart Drummond to lash it over the bar.
Macc striker Martin Gritton then tested young Shrimpers keeper Scott Loach with three shots from the edge of the box, before he wasted a penalty after Jim Bentley had barged Danny Thomas in the back.
However, he made no mistake in the 25th minute when he headed home a pinpoint cross from Gareth Evans from four yards.
But their lead was shortlived as Gary Thompson picked out the unmarked Matt Blinkhorn to stroke the ball home from 15 yards in the 29th minute.
Macclesfield teenager Christian Millar nearly marked his debut with a goal on 48 minutes, but his sharp shot on the turn was brilliantly saved by man of the match Loach.
At the other end, Brain was also in the action tipping his shot wide from Garry Hunter before making a breathtaking stop to deny a curling Baker drive.
Macclesfield were undone by a bizarre goal in the 86th minute when Maltese international Luke Dimech sliced a clearance on to his own crossbar for Thompson to crash home the rebound from six yards.