Silva, now 31, will depart when his contract expires, bringing an end to a remarkable nine-year spell at the club. During that time, he has won six Premier League titles and the Champions League, becoming one of the defining players of Pep Guardiola's era.
Speaking after City's 4-0 FA Cup win over Liverpool, assistant manager Lijnders was clear about the scale of the loss.
"Every good story comes to an end," he said. "You never replace a player with the same kind of player, because they do not exist. Bernardo Silva is unique."
Lijnders highlighted Silva's influence across every part of the game, from controlling possession to leading the team on the pitch.
"The way he controls games, the way he moves, the way he receives, the way he leads, the way he sees the solutions - all these things," he added.
City will not attempt a direct replacement. Instead, Lijnders said the focus will be on building the squad in a different way.
"You never search for a replacement of one type of player. You search for what is needed to grow with the team and somebody who can fit in the first XI," he explained.
He also pointed to the club's younger players as part of the long-term plan.
"We hope with our academy and the young players we already bought that they can make that step in midfield. But they have to grow."
Despite that, Lijnders admitted Silva's absence will be felt immediately.
"When he is not playing, you see how he is missed. That is one game. Imagine a season," he said.
Silva's consistency and intelligence have long been praised by Guardiola, who once described him as "a master" for his ability to control tempo and read the game.
That combination of technical quality and work rate made him vital to City's success. Whether in midfield or out wide, Silva delivered in big moments and set the standard for others.
Lijnders hopes the midfielder gets the send-off he deserves in his final weeks at the club.
"I hope he enjoys the last months. It is only six weeks. He deserves a good farewell and all that attention," he said.
Silva will leave as one of Manchester City's most influential players, and replacing him, as Lijnders made clear, will not be straightforward.