Rodrigo Prieto was born in Mexico City, Mexico. His grandfather, Jorge Prieto Laurens, was the 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. Prieto's grandfather escaped with his family to Texas and then to Los Angeles, where Prieto's father would spend most of his childhood. Prieto's father studied aeronautical engineering at New York University, where he met and married Prieto's mother, an artist. Rodrigo Prieto graduated from Centro de Capacitación Cinematográfica in Mexico City, where Prieto had become an established cinematographer, working with such names as Spike Lee (25th Hour), Curtis Hanson (8 Mile), Ang Lee (Brokeback Mountain and Lust, Caution) and Pedro Almodóvar (Broken Embraces). Nonetheless, his political legacy still had a visible effect on his career. In 2002, Prieto shot Frida, a film about Frida Kahlo, a Communist Mexican artist. In 2003, Prieto cooperated with Oliver Stone in two documentary projects: Comandante, about Fidel Castro, and Persona Non Grata, about Yasser Arafat. In 2004, Prieto shot Alexander for Stone. Prieto also worked with Alejandro González Iñárritu on the acclaimed Amores perros, 21 Grams, Babel and Biutiful.
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, featuring strong colors and sharp imagery blended with atmospheric yellows and browns, as well as his experimental use of infrared during a battle scene in Alexander. Prieto also is interested in evoking naturalism, most evident in The Homesman and Brokeback Mountain. Prieto not only shot Brokeback Mountain, for which he was nominated for an Academy Award for Best Cinematography, but appeared in a cameo role within the film as a Mexican gigolo whom Jake Gyllenhaal's character, Jack Twist, meets.
Prieto has formed an artistic collaboration with Martin Scorsese; first on The Wolf of Wall Street, Silence, for which he garnered his second Academy Award nomination for Best Cinematography, and most recently The Irishman, released in November 2019. In December 2019, Prieto announced he would be involved with Scorsese's upcoming film Killers of the Flower Moon. He served as cinematographer for the music videos for the three Taylor Swift 2020 singles, "The Man", which references one of his previous films, The Wolf of Wall Street, "Cardigan" and "Willow".
Prieto is the recipient of the 2021 Vilcek Prize in Filmmaking, awarded by the Vilcek Foundation.