The real guns the filmmakers intended to use were delayed at the Mexican border for two weeks, so for the first two weeks of filming only rubber prop guns were used, with all of the visual effects added digitally in post-production. At first Antonio Banderas was so thrown off by using silent prop guns that he was mouthing "bam" noises as he fired off fake shots.
The last movie Robert Rodriguez wrote as a member of the Writers' Guild of America. He left the WGA after completing the script, saying that they "have too many rules and just take your money." He would later leave the Directors' Guild of America in early 2004, before the filming of Sin City (2005).
Most of the gunfight in the church was filmed with rubber guns, almost no squibs and no physical damage to the church. Nearly all bullets, blood, explosions and physical damage were added in post-production.
The Mexican military was originally going to supply the vehicles, but when they found out that the villain was supposed to be an army general, they refused. The vehicles were supplied by local collectors.
After being introduced to High-Definition digital video by George Lucas in 2000, Robert Rodriguez made this film his personal test to push the limits of the cameras. They withstood all of the conditions, including the often intense Mexican heat, and allowed Rodriguez to experiment with various lenses, filters and frame speeds.
In the sidewalk café scene, after Johnny Depp walks away, Rubén Blades pours the first drink of his wine on the ground. This is a symbolic gesture meaning "for those who have gone before" and is a salute to his murdered partner.
Cheech Marin refers to Antonio Banderas as "the biggest Mexican ever seen.", despite Banderas being a Spaniard, not a Mexican. Banderas is 5'9", which is still taller than the average Mexican male (5'7"), but Robert Rodriguez, who is 6'2", really is "the biggest Mexican."
There are several scenes that were left over from El Mariachi (1992) and Desperado (1995). The hotel escape was originally intended for "Desperado", and the escape from the compound (while guarded in a jail cell) was included in the original script for "El Mariachi".
According to Robert Rodriguez, the idea to do a third movie in his El Mariachi (1992) franchise came from his friend Quentin Tarantino, who, knowing Rodriguez to be a fan of Sergio Leone, also suggested the title. Tarantino is given special thanks in the closing credits. Actually, however, Rodriguez intended on making a trilogy from the beginning. You can read that in his book "Rebel Without A Crew".
During pre-production, Robert Rodriguez estimated that he would need around 70 visual effects shots in the movie, but it wound up being more than 400. However, due to Rodriguez's extremely fast and efficient style of filming, and the fact that digital effects could be inserted much easier into digital video, the film could be finished within budget.
There are a few references from the graphic novels of "Sin City", which Robert Rodriguez filmed after this movie. First, when Sands shoots Ajedrez in the stomach after getting kissed by her, it's an identical picture from the graphic novel "A Dame To Kill For", which is #2 in the Sin City maxi series. Earlier in the movie, when Barillo makes Sands blind, there is almost an exact picture from the Sin City book "Hell And Back". Other similarities are the scene with El Mariachi and the priest in the confessional booth (as seen in the book "The Hard Goodbye") and the subplot involving facial reconstruction (as seen in "A Dame to Kill For").
For the final confrontation, Sands as a cowboy, dressed in all black, is a direct homage to El Topo (1970) (The Mole). Sands is blinded, bleeds out of his eyes, is left for dead and undergoes a transformation. El Topo also goes through a transformation, as he is shot stigmata-style, bleeds out of his wounds and is left for dead.
William Dafoes character is alot like the Mexican drug lord Amado Carrillo Fuentes , who actually died during a cosmetic procedure to alter his image as he was being pursued by both Mexican and US law enforcement agencies