Wigan accepted Birmingham's bid for N'Zogbia last month but the parties could not agree personal terms and the winger is now set to line up against Blues in Saturday's Premier League clash at St Andrew's.
The 24-year-old has a reputation as a difficult player to manage but Martinez could not be happier with his contribution since the deal fell through.
He said: "I think that's well in the past. The transfer window brings you that sort of speculation but once the window closed I've been very happy with the focus and concentration of the players, especially Charles.
"We forget the players are human beings and the transfer window being open while the competition is going on is really wrong.
"But I've been really pleased with his reaction, the players have been really happy with his attitude and his behaviour and the way he performed on Wednesday showed the talent that he's got.
"I don't think it's going to affect anyone. It doesn't concern me at all. What is important is the way we're starting to gel as a team."
N'Zogbia has been a key figure for Wigan since joining from Newcastle for £6million in January 2009 and he was the matchwinner again in the Carling Cup clash against Preston on Wednesday.
The half-time substitute netted the crucial goal in injury time to seal a 2-1 victory, completing a late turnaround after the npower Championship side had led with three minutes to go, and Martinez believes it could prove a very important victory.
"It's a great positive in the way we got through," he said. "It was very difficult for us and the way we reacted was really positive and the way we finished the game gave us a great feeling.
"You could see the dressing room feeling really good and you need experiences like that to develop as a team. I feel now we can take that into the league."
Wigan will certainly hope to do just that after picking up only four points from five games thus far, leaving them third bottom of the Premier League table.
If they are to add three points to that total tomorrow, they will need to end Birmingham's unbeaten home record, which stretches back almost a year.
Alex McLeish's side have proved very hard to beat since returning to the top flight and Martinez knows his side have their work cut out.
He said: "Birmingham know each other very well. They are well organised and difficult to break down from open play. It is one of the toughest places in the Premier League.
"I saw them play against Liverpool (who they held to a goalless draw in their last home league match) and they restricted them to very little.
"They have outstanding, world-class talent like (Nikola) Zigic and (Alexander) Hleb that is starting to settle in. I think it is a better squad than the one they had last season and we will need to be at our best."
Martinez is set to be without Hendry Thomas for the match after he sustained a bad cut to his shin against Preston while Tom Cleverley (knee) and club captain Gary Caldwell (hip) are also sidelined.
Caldwell has yet to play for the first team this season but he did feature in a behind-the-scenes match on Wednesday and Martinez has been surprised by the defender's quick progress.
The manager, though, does not expect Caldwell to be available for Scotland's Euro 2012 qualifiers against Czech Republic and Spain next month.
"Probably Gary needs another three or four weeks," added Martinez. "We didn't expect him to be where he is now and that's credit to him. He's been working in an incredible manner.
"He's always had in his head that he wanted to be available to play for Scotland. I think that's a little bit too early but he's not too far away."