The Irishman was a standout performer for Wolves last term, making 45 appearances in all competitions as the Molineux-outfit finished seventh in their first season back in the Premier League, while simultaneously reaching the semi-finals of the FA Cup.
With the Europa League to deal with, Nuno has seen his squad stretched already this season and his side perhaps fell victim to fatigue in Sunday's 3-2 defeat at Everton. Adama Traore again featured at right-wing-back, with Doherty having previously been eased back into the action following a knee injury that troubled him over the summer.
The 27-year-old has completed 90 minutes in just one of his four outings so far this term and Nuno has confirmed he will not be part of his country's plans for their upcoming Euro 2020 qualifier against Switzerland and friendly with Bulgaria.
"No, he's going to stay, he has to have a small surgery for something that is bothering him," Nuno said.
The boss was reluctant to disclose the nature of the surgery but sources in the local media have speculated that it could be a non-football related issue.
Nuno says it is a problem that has been troubling the Dubliner for some time and the club have chosen the first international break of the season as the perfect time to send him for surgery, especially with Traore adapting well to his new role.
The Portuguese coach is unsure how long he will be absent for, but is pleased that it will also give the player extra time to get over his knee problem.
"I don't know, but we've been speaking about Matt since a long time ago," he added. "He's getting back and we have to give him time to recover well from the pain he has in his knee."
Wolves started the Premier League season with three draws before going down to their first defeat of the campaign at Goodison Park on Sunday.
Having also qualified for the group stages of the Europa League, they have certainly been busy and those not called away on international duty will be looking to rest their weary muscles ahead of their return to domestic action.
Next up in the league is the visit of Chelsea to Molineux on September 14, before they kick off their European pool programme with the visit of Braga five days later.