Local born McGleish spent three years scoring regularly for Barnet before working his way to Northampton where he has continued to find the back of then net. His 12th goal of the season settled this match shortly into the second half.
It had started very differently as Barnet got off to a flyer. Dean Sinclair headed just wide and they had a decent penalty appeal turned down inside the opening minute.
Anthony Charles headed wide from a free-kick, but then Northampton started to take control.
The first warning shot was fired by McGleish, who had an effort disallowed for offside in the 21st minute.
A Josh Low header was comfortably saved by Ross Flitney in Northampton's next attack before the Barnet keeper was put under even more pressure.
Northampton had to survive a series of handball penalty appeals in between a run of good efforts from midfielder Martin Smith.
He had one spectacular effort well saved by Flitney, another deflected wide for a corner and a 25-yard power drive that whistled just a few feet wide of the Barnet goal.
Northampton really began to turn the screw at the start of the second half and they went ahead through McGleish's penalty two minutes after the restart.
Fellow forward Junior Mendes won the spot-kick when his skills drew a foul from Damien Batt, who was booked.
Then McGleish stepped up to bury a low shot into the right-hand corner of Flitney's goal before celebrating in front of the travelling Northampton fans.
Barnet were fortunate not to fall further behind moments later when David Rowson got past Flitney only to trip up with the goal at his mercy.
Northampton almost paid for those missed opportunities as Barnet forced a couple of late chances, but they ultimately finished as worthy winners and could have won by a wider margin.