McGleish might have given up the captaincy, which went to Chris Doig, after the former Colchester striker was placed on the transfer list before Christmas. But the ultra busy McGleish still led by example as he took his tally of goals in a Cobblers shirt to 51.
McGleish reached his 50 landmark in first half injury time when he headed home from just a couple of yards after an initial header by Ian Taylor from a Eoin Jess cross had been well saved by Shane Higgs and the first rebound effort from Luke Chambers hit the crossbar.
Northampton had not been awarded a penalty at home for 13 months, but McGleish made certain of the home points by scoring from the spot 16 minutes from time after Robin's skipper John Finnigan had been adjudged to have handled a volley by Jess.
McGleish gleefully buried the spot-kick and, such has been the nature of Northampton's struggles in front of their home fans this season, that this was the first time they had scored more than one at home in a league or cup match.
The victory also provided a boost for the caretaker management duo of Ian Sampson and Jim Barron who took over a week ago following the resignation of John Gorman.
Northampton's first win in seven matches meant Cheltenham stayed below them in the League One relegation zone and the Robins have now lost their last five matches on their travels.
The visitors started brightly with JJ Melligan heading a Brian Wilson cross just wide of the target, while home goalkeeper Mark Bunn was called upon to make an excellent flying save to his left to keep out a seventh minute volley by Steve Guinan.
But Cheltenham's sparkle didn't last and they rarely threatened the home goal again until 18 minutes from time when substitute Sosthene Yao fired in from 20 yards along the ground and the ball grazed the post as it flashed narrowly wide.
Bunn was again called upon to save a Damian Spencer volley in injury time but by then Northampton were celebrating their second home win of the season.