Former Northampton striker Luke Norris scored the only goal as Colchester United saw off the Cobblers.
Norris, who played on loan for Northampton in 2013-14, struck a second half penalty to win the game.
Victory was Colchester’s first of the new season. By contrast, Northampton were unable to build on their midweek win at Swindon, and they have now lost 3 of their opening 5 League 2 matches.
The Cobblers had made a positive start in Essex, with Sam Hoskins was denied by Dean Gerken. Ryan Clampin also had to be on hand for the hosts, as the defender blocked a header from Vadaine Oliver.
Colchester had more pressure as the game continued. David Cornell was called upon to keep out Jevani Brown near the end of the first half, and another to deny Luke Gambin the second period.
The only goal would come from the penalty spot. Ben Stevenson was fouled by Shaun McWilliams, and from the spot, Norris beat Cornell.