Patrick Warburton improvised when Kronk hummed his own theme song when he was carrying Kuzco in the bag to the waterfall. Disney legal department had Warburton to sign all rights to the humming composition over to them.
In the scene where Kuzco and Pacha are searching through the various potions, Pacha says, "Lions, tigers, bears" then when they come upon the potion for humans, it is missing and Yzma says "oh my." Together this creates a line from The Wizard of Oz (1939). According to producer Randy Fullmer and director Mark Dindal, they were forced to use this joke, which they detested, by then-head of Feature Animation Thomas Schumacher.
Two subtle visual jokes: when Yzma pours the "drink" into the cactus plant, after Kuzco's neck transforms, the cactus turns into the shape of a llama. When Kronk is trying to hide in the background with Kuzco in the bag, the scene pulls back to reveal a painting of two figures pointing at Kronk.
In the scene where Pacha is carrying Kuzco through the jungle, Pacha and Kuzco discuss Kuzco having low blood sugar. This is an in-joke about the fact that David Spade, who plays Kuzco, is hypoglycemic in real life.
The makers of the film originally wanted to get Sting to sing the opening song but he said he was too old, they needed someone more hip and younger. So they went with Tom Jones, who is 11 years older than Sting. He did write "My Funny Friend and Me", which included a music video from the movie.
This film was originally planned to have been a dramatic, sweeping Disney musical named "Kingdom of the Sun", to be directed by The Lion King (1994) director Roger Allers and Mark Dindal, director of Turner's Cats Don't Dance (1997), with six original songs written by Sting, that was essentially an Incan re-telling of Mark Twain's "The Prince and the Pauper." David Spade was the voice of the young emperor Manco, Owen Wilson was Pacha, a young peasant with a striking resemblance to the emperor, and Eartha Kitt was Yzma, the aged royal sorceress. The film involved Manco and Pacha switching places, except that Yzma finds out, turns Manco into a (non-speaking) llama, and makes Pacha do her bidding. Pacha also eventually was to fall in love with Nina (voice of Carla Gugino), the emperor's betrothed. The resulting film tested very poorly, and the production was suspended, even though the film was 50% complete. Allers and Yzma supervising animator Andreas Deja both left the project and moved to Orlando, Florida to work on Lilo & Stitch (2002). During the production hiatus, Dindal, producer Randy Fullmer, story man Chris Williams, and screenwriter David Reynolds completely overhauled the film, eventually throwing out Wilson, the "Prince and the Pauper" angle, the completed footage, and all but one of Sting's songs. As Roger Allers's take on the film was starting to take shape, Disney management were becoming increasingly uncomfortable with the film, feeling it was too similar to the story of the Prince and the Pauper. Test screenings too generated poor feedback. On the strength of this, Mark Dindal was hired to add more comedic elements to the film. Dindal and Allers did not get on and essentially both began making their own separate version of the film. The Disney executives, although unhappy with Roger Allers's direction on the film, held off from interfering with him, given that he had provided them with their biggest hit, The Lion King (1994), which too had had a troubled production. Also, most of Allers's crew were very loyal to their director. By the summer of 1998, it was increasingly clear that "Kingdom of the Sun" was not going to make its summer 2000 release date. Merchandising tie-ins with McDonalds and Coca-Cola amongst others meant that the release date could not be moved. Director Roger Allers asked for a six month extension to the release which was denied. Allers then quit the project. With the film on the brink of total shutdown, co-director Mark Dindal worked on a retooling of the film. While he did this, most of his animators were reassigned to work on the Rhapsody in Blue segment of Fantasia 2000 (1999). The result of this retooling was the film we have today. The story was rebuilt from the ground up, retaining Spade's and Kitt's characters and creating a new, wackier film that centered around Spade's (talking) llama, Yzma, and two new characters: Pacha, now a middle-aged man played by John Goodman, and Kronk.
Sting's wife Trudie Styler made a documentary about the troubled making of the film as part of the deal that involved her husband working on the film. Her completed documentary, "The Sweatbox", is owned by Disney and can be watched online on vidme.
Because of the allusion in the title, the movie is often wrongly described as a version of "The Emperor's New Clothes" by Hans Christian Andersen. While some character traits of the main character are similar to the title character in Andersen's story, there are no further connections. Instead, the story shares much more similarities with the fairy tale "Kalif Storch" (Caliph Stork) by Wilhelm Hauff.
In the dinner scene where Kronk lights a pair of candles the holder is of a small figure. This was a character from the early versions of the film. He was an advisor to the emperor that was later written out.
The sequence when the fly hits the spiderweb and gets eaten, the fly screams "help me" in the same way as the movie Classic The Fly (1986), the fly happens to hit the web too and gets eaten by the spider, as it screams the same "help meeeeeee".
To keep the animation team together as a crew during the production hiatus, former Disney animator Eric Goldberg was allowed to borrow the animation crew to help produce his independent film Rhapsody in Blue (2000), which Disney ended up inserting into Fantasia 2000 (1999) as one of the musical segments.
The cut-away to the chimp with the bug, is a subtle reference to one of the opening shots of the film Citizen Kane (1941). During the opening montage of the Xanadu Estate, there is a similar shot of a pair of monkeys eating bugs.
During the film's troubled production, one of the Disney executives stormed into producer Randy Fullmer's office and, placing his thumb and forefinger a quarter-inch apart, angrily remarked, "Your film is this close to being shut down."
In the final chase, Cuzco and Pacha run down a curling stone staircase ahead of the now-transformed palace guard. The shadows of the octopus-guard are thrown on the wall at the head of the stairs. The whole image is an homage to the iconic "Sorcerer's Apprentice" scene in Fantasia (1940)
During production, back when the movie still bore the title "Kingdom of the Sun", Hungarian animation director and folklore expert Marcell Jankovics was brought over to Disney to help out with the project. He considered the proposed story similar to his feature film debut Johnny Corncob (1973), and he has already had considerable experience in adapting the tales of older cultures and folklore in works such as Fehérlófia (1981) and the Hungarian children's series Magyar népmesék (1980). When co-director Roger Allers quit and the movie took a drastic change in direction, Jankovics also left the project after only having worked on it for a few months. Though Jankovics reportedly hated the completed film, he claims he had made several good friends at Disney. He used his working fee to fund his film Az ember tragédiája (2011).
The trivia items below may give away important plot points.
The original ending was of Kuzco building his huge summer home on the hill next to Pacha. Sting sent a note to the producers objecting that Kuzco has not really changed or learned from his experiences if he still built his excessive mansion. Kuzco instead builds (and enjoys) a much smaller hut that is more appropriate to the village and the peasant's way of life.
When Kronk and Yzma go to their secret lab, they pass several animal-shaped gates. The first one is a cat and the sound of a cat meowing is heard; ironically, Yzma is turned into a cat by the end of the film. This is a respectful nod to Eartha Kitt's famous role as Catwoman in the televised Batman (1966) series.