Paul Cook says Will Grigg will 'forever be a part of Wigan's history'.
The 27-year-old arrived on Wearside yesterday after sealing a bumper three-and-a-half year contract with Sunderland.
The two clubs finally reached an agreement in the final moments of the January window.
His departure has left Wigan supporters bitterly disappointed.
There was no time for the club to replace the Northern Irish striker, who has become a cult figure over two promotion campaigns and a famous FA Cup run.
"I’m disappointed obviously, for a lot of reasons, for Will’s relationship with the staff, the players and the supporters," he said.
"But I’m also happy in a way for Will, because being a footballer is a small window of your lifetime.
“I also respect Sunderland as a club, and it’s something I’m not going to get involved in, the amount of bids etc.
“We wish Will well, and we certainly did our best to keep him.
"To say it’s left a bit of a cloud on the club is an understatement, but that’s football," he added.
"Players and managers come and go, and that’s football.
“This football club will be here forever, and Will Grigg will forever be a part of its history.
“He’s an absolute diamond of a bloke and he’ll always be welcomed back here.”
Cook says Wigan 'did their best' to keep Grigg at the club.
“I totally understand and empathise with the emotions the supporters will be going through,” he said.
“As manager, I was hoping the window would come and go, we were happy with what we’d done business-wise.
“You’re sat in the office on deadline day, and the first instinct is to protect what you’ve got, as much as you can.
“But unfortunately in football - and I said this all along - everyone has a price, and contracts and stuff have to come into it.
“We did our best, we really did, but as a club, and as a manager, when offers of this magnitude come in, you have a decision to make and the boy has a decision to make.
“What we do with the money is in the future.
“What’s important right now is to respect Will, and understanding that sometimes football is a cruel world.
“To have turned down the size of bids we did showed we weren’t looking to sell players.
“But sometimes you have to make decisions, and the people who made that decision did so with the best interests of the club at heart - and that should never be forgotten.”