Principal photography
In 2006, shortly before the U.N. Headquarters underwent major renovations, Del Toro and Soderbergh shot the scenes of Guevara speaking to the U.N. General Assembly in 1964. The director wanted to shoot the first part of The Argentine in Cuba but was prevented from travelling there by the U.S. government's embargo. Doubling Santa Clara proved to be difficult because it was a certain size and had a certain look. Soderbergh spent four to five months scouting for a suitable replacement, looking at towns in Veracruz/Yucatán before settling on Campeche, which had the elements they needed.
The original intention was for The Argentine to be shot using anamorphic 16 mm film because, according to the director, it needed "a bit of Bruckheimer but scruffier". He kept to his plan of shooting The Argentine anamorphically, and Guerrilla with spherical lenses. Soderbergh wanted to use the new RED One rather than 16 mm film because of its ability to replicate film stock digitally but initially, it was not going to be available on time. However, their Spanish work papers and visas were late and Del Toro and Soderbergh were grounded in Los Angeles for a week. The director was meanwhile informed that the prototype cameras were ready.
Each half of the film focuses on a different revolution, both fundamentally the same in theory but vastly different in outcome, reflecting the Marxist notion of dialectics. Soderbergh wanted the film's two parts to mimic the voice of the two diaries they were based on; the Cuban diaries were written after the fact and, according to the director, "with a certain hindsight and perspective and a tone that comes from being victorious", while the Bolivian diaries were "contemporaneous, and they're very isolated and have no perspective, at all. It's a much more tense read, because the outcome is totally unclear".
Soderbergh shot the films back-to-back in the beginning of July 2007 with Guerrilla shot first in Spain for 39 days and The Argentine shot in Puerto Rico and Mexico for 39 days. The director conceived The Argentine as "a Hollywood movie" shot in widescreen scope aspect ratio, with the camera either fixed or moving on a dolly or a Steadicam. Guerrilla was shot, according to Soderbergh, "in Super-16, 1.85:1. No dollies, no cranes, it's all either handheld or tripods. I want it to look nice but simple. We'll work with a very small group: basically me, the producer Gregory Jacobs and the unit production manager". According to the director, the portion set in Cuba was written from the victor's perspective and as a result he adopted a more traditional look with classical compositions, vibrant color and a warm palette. With Guerrilla, he wanted a sense of foreboding with handheld camerawork and a muted color palette. Soderbergh told his production designer Antxon Gomez that the first part would have green with a lot of yellow in it and the second part would have green with a lot of blue in it.
At the end of The Argentine, Soderbergh depicts Guevara's derailment of a freight train during the Battle of Santa Clara. In filming the sequence, Soderbergh balked at the digital effects solution and managed to reallocate $500,000 from the overall $58 million budget to build a real set of tracks and a train powered by two V-8 car engines. To film the scene, they had six rehearsals, and could only shoot the scene once.
Many aspects of Guevara's personality and beliefs affected the filming process. For instance, close-ups of Del Toro were avoided due to Guevara's belief in collectivism, with Soderbergh remarking, "You can't make a movie about a guy who has these hard-core sort of egalitarian socialist principles and then isolate him with close-ups." According to Edgar Ramirez, who portrays Ciro Redondo, the cast "were improvising a lot" while making The Argentine, and he describes the project as a "very contemplative movie", shot chronologically. While filming outdoors, Soderbergh used natural light as much as possible. Del Toro, who speaks Puerto Rican Spanish, tried to speak the best Argentinean Spanish (Rioplatense Spanish) he could without sounding "stiff". Prior to shooting the film's final scenes that depict Guevara's time in Bolivia at the end of his life, Del Toro shed 35 pounds to show how ill Guevara had become. The actor shaved the top of his head rather than wear a bald cap for the scenes depicting Guevara's arrival in Bolivia in disguise.
Soderbergh has said that with Che, he wanted to show everyday tasks, "things that have meaning on a practical level and on an ideological level", as a "way of showing what it might have been like to be there". While addressing the issue after at the Toronto International Film Festival, Soderbergh remarked that he was trying to avoid what he felt were typical scenes for a biographical film and that he would tell screenwriter Peter Buchman, that he was "trying to find the scenes that would happen before or after the scene that you would typically see in a movie like this". Soderbergh was not interested in depicting Guevara's personal life because he felt that "everybody on these campaigns has a personal life, they all left families behind, that doesn't make him special and why should I go into his personal life and nobody else's?"
Soderbergh decided to omit the post-revolution execution sentences of "suspected war criminals, traitors and informants" that Guevara reviewed at La Cabana Fortress because "there is no amount of accumulated barbarity that would have satisfied the people who hate him". Soderbergh addressed the criticism for this omission in a post-release interview where he stated: "I don't think anybody now, even in Cuba, is going to sit with a straight face and defend the events. La Cabana was really turned into a Roman circus, where I think even the people in power look back on that as excessive. However, every regime, in order to retain power when it feels threatened, acts excessively ... This is what people do when they feel they need to act in an extreme way to secure themselves". The filmmaker noted as well that, "with a character this complicated, you're going to have a very polarized reaction". Furthermore, he was not interested in depicting Guevara's life as "a bureaucrat", stating that he was making a diptych about two military campaigns, declaring the pictures "war films". Soderbergh said, "I'm sure some people will say, 'That's convenient because that's when he was at his worst.' Yeah, maybe—it just wasn't interesting to me. I was interested in making a procedural about guerrilla warfare".
Soderbergh described the Cuban Revolution as "the last analog revolution. I loved that we shot a period film about a type of war that can't be fought anymore". Soderbergh said he was open to making another film about Guevara's experiences in the Congo but only if Che made $100 million at the box office. It did not.