Donald Alex MacKillop – known as Splash – died at his home in Berneray off North Uist just days after undergoing an operation for cancer.
Mr MacKillop, 78, lived all his life on Berneray where, in 1987, the prince came to stay for a week to learn about crofting. He planted and lifted potatoes, cut peat, helped dip sheep and planted trees on the 92 acres of arable croft.
Prince Charles said he was "deeply saddened" to hear of Mr MacKillop's death. He said: "I shall never forget the time I spent with him and his wife on Berneray and the important role he played on the islands.
"People like him are very hard to replace."
The prince stayed twice with Mr MacKillop and his wife Gloria, and returned in 1991 to make a BBC documentary, A Prince Among Islands, with Selina Scott.
He told islanders that he found crofting inspirational, as it was close to his philosophy on agriculture. He is said to have put his experience to use on his organic farm at Highgrove.
The royal visitor returned to the island in 1999, when he joined the 140 residents to officially open the 7 million causeway to North Uist.
The MacKillops turned their home, Burnside Croft, into a B&B after the last of Prince Charles's visits. Guests were able to stay in the same room as royalty and see his signature in the visitor's book.
The couple also kept in regular touch with the prince, exchanging letters and meeting up at official functions.
Alex MacDonald, convener of Comhairle nan Eilean Siar (Western Isles Council), also paid tribute. He said: "Splash was a larger-than-life character and his many friends across the islands will be saddened by today's news."