Voice artists in animated movies usually record their parts alone, with no other actors or actresses in the studio with them. In a break with this tradition, Kevin Kline and Sir Kenneth Branagh recorded their dialogue together similar to when Disney's Aladdin (1992) had Jonathan Freeman record many of his scenes with Gilbert Gottfried.
A series of sequels featuring Miguel, Tulio, Chel, Altivo, and even the armadillo going after other legends about gold was planned, similar to the Shrek (2001) film franchise, but following the disappointing box-office results, they were immediately cancelled.
The aesthetics of El Dorado and its inhabitants are a mixture of different pre-Hispanic cultures of Central America, in order to avoid connecting El Dorado to any particular geographical place. So, the buildings and temples are a composition of the Mixteco city of Mitla, in modern Oaxaca, Mexico, and the Mayan city of the Palenque. The features of the locals are distinctly Mayan, as well the murals and the Xibalba tradition. The weapons, attires, and human sacrifices customs are mostly of Aztec origin. Curiously, even though the inspiration comes from Central and Southern Mexico, the most widely accepted location for the real El Dorado legend was the Amazonian rain forest.
This movie shares several attributes of its namesake, the "Road" comedies made famous by Bob Hope and Bing Crosby during the 1940s (which helps explain anachronisms, such as shared language, pop culture references, and lack of historical accuracy). In homage to the veteran comedians, during the song "It is Tough to be a God", Tulio and Miguel look into a rippling bowl of liquid. The reflection of Miguel briefly takes on the pronounced ears of Bing Crosby, while the reflection of Tulio morphs into the distinctive profile of Bob Hope.
The Backstreet Boys performed "Friends Never Say Goodbye" with Sir Elton John on the soundtrack, but not in the movie. In that same year, A.J. McLean could not perform with the other Backstreet Boys for London's Party in the Park concert tour because his grandfather had surgery. For that reason, Elton temporarily replaced him.
While Tulio, Miguel, and Altivo are lost at sea, a large shark comes up out of the water in the fashion of the classic Jaws book cover and movie poster. Jaws (1975) was directed by Steven Spielbeg, who is one of the co-founders and principals of DreamWorks, which produced this movie.
The producers wanted Antonio Banderas to voice the part of Tulio, but he refused the part for undisclosed reasons. He would go on to voice Puss in Boots in DreamWorks Animation's "Shrek" film series and its holiday television specials as well as the character's solo theatrical film.
In late 1996, Tim Rice and Elton John were asked to compose seven songs, which they immediately worked on. In February 1999, before the release of Elton John and Tim Rice's Aida, it was announced that ten songs had been composed for El Dorado. It was also announced that the release date had been pushed to March 2000.
The name of the horse, Altivo, is generally interpreted as "proud" or "haughty" in modern Spanish. However, in older, more traditional usages, it means "high" or "elevated", possibly a reference to the heroes' "elevated" state to supposed godhood.