During a particularly rowdy night of production, Klaus Kinski, irritated by the noise from a hut where cast and crew were playing cards, repeatedly fired with a Winchester rifle into it. One of the bullets took the tip of an unnamed extra's finger off. Werner Herzog immediately confiscated the weapon and it remains his property to this day.
Many of the scenes were unrehearsed and unstaged, blurring the line between the cast acting in character and simply reacting to their situations. In one opening scene, when the carriage holding Ursúa's mistress tips over and threatens to collapse, a hand comes in from the right side of the frame to assist the actors in steadying their hold. That hand belongs to director Werner Herzog.
According to Werner Herzog's commentary, he paid the men who were to provide the monkeys at the end of the film only half of what they asked for, thinking they would try to run off with the money. The dealers took the money, then sold the monkeys to someone else, and prepared to fly them to Florida. In desperation, Herzog pretended he was a veterinarian and said the monkeys didn't have their vaccination documents. After filming, he released the monkeys into the wild.
The complete crew consisted of eight people.
In 1971, while Werner Herzog was location scouting for the film in Peru, his reservation on LANSA Flight 508 was cancelled due to a last-minute change in itinerary. The plane was later struck by lightning and disintegrated, with one person surviving after a free fall. Almost 30 years later, Herzog made Les ailes de l'espoir (1999), which explored the story of survivor Juliane Koepcke.