His grandfather was mayor of Mexico City and leader of the Chamber of Deputies of Mexico, but was later persecuted by the country's ruler because of political differences. The grandfather escaped with his family to Texas and then to Los Angeles. There, Prieto's father would spend most of his childhood. He studied aeronautical engineering in New York, where he met and married Prieto's mother. They moved back to Mexico, where Prieto was born. Prieto has become an established cinematographer, working with such big names as Spike Lee (25th Hour) and Curtis Hanson (8 Mile), but his Mexican political legacy still has a visible effect on his career. In 2002, he shot Frida, a film about Frida Kahlo, a communist Mexican artist. In 2003, he cooperated with Oliver Stone in two documentary projects: Comandante, about Fidel Castro, and Persona Non Grata, about Yassir Arafat. In 2004, he shot Alexander for Stone. Prieto also worked with Alejandro González Iñárritu on the acclaimed Amores Perros, 21 Grams and Babel .

Rodrigo Prieto is noted for his unconventional use of the camera often combined with strong moody lighting. In 25th Hour, Prieto utilized overexposure and other techniques to create original dream-like images to signify that the events shown on screen are memories or visions. Similarly innovative photography could be spotted in Frida, which featured strong colors and sharp imagery blended with atmospheric yellows and browns.

Recently, Prieto not only shot Brokeback Mountain, for which he has garnered an Academy Award nomination for Best Cinematography, but appeared in a cameo role within the film as a Mexican gigolo whom Jake Gyllenhaal's character, Jack Twist, meets. His most recent project was for Babel.