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Fernandes has signed an extension at Old Trafford that'll make him one of the club's highest earners until 2026, with an option for a further year.
The 27-year-old has been a key player since arriving from Sporting CP in 2020 but Merson is shocked at the timing.
He told Sky Sports: "I'm flabbergasted if I'm being honest. You give him a four-year extension, more money, a manager comes in he might not like Fernandes, he might not like all the throwing the hands up, the moaning that he does when he doesn't get the ball.
"He might have someone, it might be the lad at Ajax [Erik ten Hag], who's got someone else and thinks 'I've got someone who I want to bring in who wants to play my way'.
"I'm completely and utterly shocked. I cannot believe what's happening. Everything is just being done off the cuff. It's been being done off the cuff for the last couple of years at Man United."
Fernandes will now earn £250,000-per-week compared to his last contract which was worth £120,000-per-week.
It makes him one of United's highest earners ahead of Marcus Rashford and captain Harry Maguire.
Fernandes' performances have dipped this season but there's no denying his status as one of the Premier League's best.
Only Mohamed Salah and Harry Kane have been involved in more goals since he moved to England.
The Portugal international would likely be welcomed by any manager who takes over from Ralf Rangnick in the summer.
Ten Hag and Mauricio Pochettino are the two frontrunners right now but a decision isn't imminent according to sources.
United currently sit sixth in the Premier League and four points behind fourth place Arsenal.
Mikel Arteta's men also have a game in hand and look favourites to qualify for next season's Champions League.
The Red Devils haven't won a trophy for five years and it's their longest barren run in 40 years.
Fernandes is hoping to change that, having already suffered Europa League final heartbreak last year.
He told United's official website: "Even after two years, it still feels amazing to step out at Old Trafford, to hear the fans sing my song and to score in front of the Stretford End. It is a true privilege to wear this shirt and to fight for our incredible club.
"There is so much more that I want to achieve here, and I know that is the same for the rest of the squad and staff. More than anything, we want to give the fans the success that they deserve.
"We have shared some great moments over the last years, but the best is yet to come from myself and this team."