Hormel Foods Corporation, makers of Spam, sued the film production company for making the name of a warthog character "Spa'am". Their suit was defeated on September 22, 1995. The judge noted that "one might think Hormel would welcome the association with a genuine source of pork."
After Jim Henson's death, Rowlf the Dog was not recast for several years, as he was considered the character closest to Henson's actual personality (even more so than Kermit the Frog). In this film, Rowlf appears, but does not speak, in the first scene set in the Tavern.
Brian Henson was nervous that the whole cast and crew would get motion sick as the ship rolled on the gimbals. He gave everyone seasickness pills for the first day of the shoot, and not only did the cast and crew not get seasick but they almost fell asleep on the job.
Brian Henson said that Frank Oz was not originally a fan of Fozzie Bear's "Mr. Bimble" (the man who lived inside of Fozzie's finger). However, by the end of filming, Oz decided that it was one of his favorite jokes.
In the original script, Polly Lobster's role was played by a sultry female parrot who flirted with Silver (a similar character had been used in a sketch of The Muppet Show (1976) starring John Cleese as a pirate). When this got "too weird", according to Brian Henson, she was replaced with a male parrot named Stevenson (after Robert Louis Stevenson) who pointed out the changes made from book to movie. Stevenson was replaced by Polly Lobster for the film, but later showed up in the PC game based on the film.
Frank Oz was unable to perform and puppeteer his signature characters of Miss Piggy, Fozzie and Sam the Eagle, as he was busy directing Bowfinger (1999). Kevin Clash took over principle puppeteering duties during shooting, and Oz re-recorded the characters' voices in post-production. Oz had already participated in a recorded read-through of the script; Clash used these recordings to help prompt his performances. According to Clash, Oz gave him a brief description of each of his characters prior to shooting. Oz described Miss Piggy as "a truck driver wanting to be a woman", and Fozzie Bear as somebody similar to Jerry Lewis.
While searching for the treasure map in Billy Bones' trunk, Gonzo and Rizzo happen upon a copy of Diplomacy by Henry Kissinger. Alex Rockwell, who headed project development for the film, is his daughter-in-law.
After the success of The Muppet Christmas Carol (1992), Jim Henson Productions decided to cast Kermit and friends in another period piece. According to Kirk Thatcher, it was a toss up between a Treasure Island adaptation, or a take on King Arthur.
Ellis Flyte: The wife of Brian Henson (the film's producer and director) gives an uncredited appearance as Big Fat Ugly Bug-Faced Baby-Eating O'Brian (a female ship's crew mate seen only during the Roll Call scene).