His Morecambe side fell to defeat as the hosts completed a fourth win in six games.
It was Morecambe who started brightest at Edgeley Park, but it took eight minutes for ether side to create a half-chance. Carl Baker tried an audacious chip for the visitors, but the ball dropped just over the crossbar.
However, a minute later the hosts took the lead. Adam Griffin crossed in low from the left and there was Anthony Elding, who touched his 12th goal of the season home at the near post.
The goal inspired Stockport and within minutes Anthony Pilkington shot wide, Liam Dickinson saw a shot blocked and Elding fired narrowly over.
At the other end Morecambe defender David Artell somehow missed from just six yards out, but Stockport remained on the offensive for the large part and Elding again went close with a rising drive.
Dickinson screwed a shot inches wide following a decent cross from Jason Taylor, but Morecambe started to creep back into the game and Garry Thompson volleyed wide from 15 yards.
Their rally was halted on 40 minutes though, when the hosts doubled their lead. Greg Tansey swung in a free-kick and Dickinson planted home a simple angled header.
Craig Stanley curled the first effort of the second half wide as the visitors
sought a way back into the game, but Stockport hit back with Pilkington seeing a shot blocked and Elding only narrowly failing to connect with Griffin's cross-cum-shot.
Matt Blinkhorn finally grabbed McIlroy's men a lifeline on 80 minutes when he headed home, but it wasn't enough for the visitors.