The building that houses the Ché Café was constructed as part of Camp Calvin B. Matthews, the Marine Corps rifle range that occupied the Torrey Pines mesa from 1917 to 1964. When the Marine Corps decommissioned the camp and transferred the land to UC San Diego, most of the buildings were demolished. A few survived, absorbed into the new campus. The structure that became the Ché Café served as a mess hall for Marines during the decades when more than a million men came through the rifle ranges. The transition from military mess hall to student cooperative — from a space organized around discipline and hierarchy to one organized around collective decision-making and radical politics — captures something about what happened to this particular patch of California mesa in the second half of the twentieth century.

The Ché Café opened in 1980 as a student organization affiliated with UC San Diego's college system. Its name references Ernesto 'Che' Guevara, but students also created a backronym: Cheap Healthy Eats. Both meanings are accurate. The café has always served affordable vegetarian and vegan food, operated by volunteers and workers rather than paid management, with prices calibrated to what students can actually afford. The food and the politics have been intertwined from the beginning — the idea that eating should be accessible and that the people making the food should have a say in how the enterprise is run reflects the cooperative economics the café has practiced for more than four decades. It has been worker-owned and collectively managed throughout its existence.

The Ché Café became a significant venue in the Southern California DIY music scene beginning in the 1980s, when the punk and hardcore movements were creating their own infrastructure outside commercial music venues. All-ages shows, local and touring bands, door prices that matched the café's food prices — the Ché Café offered a space for music that wasn't primarily organized around profit. Zack de la Rocha has cited the café as formative. Hundreds of bands passed through over the decades, some of them going on to wider recognition, most of them playing to small rooms and driving home afterward. The Ché Café's role in San Diego's music history is not measurable in ticket sales; it is measurable in the music that was made possible by having a place to play.

The university has made several attempts to close or evict the Ché Café. A major conflict arose in 2014 when UC San Diego sought to end the café's space license; students and alumni organized in response, and the immediate closure was avoided. Further disputes occurred in 2017. The café's supporters have argued, with some justification, that the Ché Café represents a form of student governance and cooperative economics that serves educational and community purposes the university's formal structures do not. The café has survived by building enough community support that closure would be politically costly. It is, in the end, a small wooden building on a research university campus, serving cheap food and booking punk bands — and somehow this has been sufficient to keep it standing for more than four decades.