German retail VHS version was cut by ca. 6 minutes to secure a "Not under 16" rating. This version was also used for TV broadcasts.
Reportedly, Desperado suffered severe cuts when initially submitted for an R-rating. The end sequence originally involved a large scale shootout between El Mariachi, Carolina, Bucho & his thugs. After seeing the amount of footage that needed to be trimmed, the director opted to delete the entire scene which currently ends in a slow-mo of Banderas blasting away. 2 additional scenes were also removed featuring the "crotch-gun" (seen in the guitar case) used during 2nd bar shootout and the same gun going off accidentally when Banderas is in bed with Hayek. This gun was later used for a scene in From Dusk Till Dawn.
Certain TV edits of the film make humorous changes to dialogue, including the changing of the sentence, "What the f**k?!" to "What the frijoles?" ("Frijoles" is Spanish for "beans.")