Opposition view: Martin praises impressive Cobblers and admits MK Dons 'got away with one'
Cobblers were unfortunate to be behind at half-time after an even opening 45 minutes but came out all guns blazing in the second-half and turned the contest on its head.
Ryan Watson and Peter Kioso added to Fraser Horsfall's early opener to give Town a 3-2 lead with 12 minutes to go, but Cameron Jerome levelled before Charlie Brown grabbed victory.
"I'm really pleased we won but we've still got a lot to learn," said Martin. "We can't be that poor again because we got away with one there.
"It's difficult because we were playing a team who had real belief in their new manager and what they're doing. They had real intensity and desire and they're enjoying themselves and you could see that.
"They scored the early goal and they sensed they had a chance and went really aggressive. We adapted well in the first-half and I thought we looked dangerous but the goal straight after half-time kills the flow and they were even more aggressive.
"Credit to Northampton, I thought they were great today and they will feel really unlucky not to win the game, let alone draw it, because we gave them way too many chances. Credit where credit's due but we found a way.
"What I would say is that we would have lost that game not so long ago so to show that mentality and that character is something they need to keep building on. Their resilience is growing all the time."
Martin was particularly unhappy about the nature of the goals Dons conceded, two of them coming from free-kicks.
He added: "It was a really sloppy goal to start with and then we concede from another set-piece. The goals we conceded today hurt me and we let ourselves down, but we showed unbelievable intensity and character to get back into the game.
"The substitutions came on and made a huge impact and we needed that new energy and fresh legs and I'm really pleased that Charlie (Brown) won the game for us because he deserves it for how hard he's worked."