Lofthouse made more than 450 appearances for the Trotters, scoring 255 goals for the club between 1946 and 1960. He also represented England 33 times and scored 30 goals.
Bolton announced Lofthouse had died peacefully in his sleep at his nursing home on Saturday night. Chairman Phil Gartside told www.bwfc.co.uk: "On behalf of everyone at Bolton Wanderers Football Club, I would like to extend our deepest condolences to Nat's family, who are very much in our thoughts at this time.
"Nat undoubtedly is a Bolton Wanderers legend. He was a one-club man and our football club meant as much to him as he did to us.
"We will miss him but we will celebrate his life, his legacy and great times that he brought to Bolton Wanderers."
After finishing playing, Lofthouse remained at the club in a number of off-field positions including chief coach, chief scout, caretaker manager and club president, in which he remained until his death.