Trujillo was born in Santa Monica, California, on October 23, 1964. He is of Mexican and Native American descent. He grew up in Culver City, California, where his father was a teacher at Culver City High School. Trujillo garnered interest in music during his childhood; his mother was a huge fan of Motown, particularly musicians like Marvin Gaye, James Brown, and Sly and the Family Stone. Trujillo stated that “Jaco [Pastorius] was my hero growing up”, and that the iconic jazz bassist changed his view of what the instrument could play: “Hearing him was like hearing Eddie Van Halen doing “Eruption” for the first time: You thought, ‘What instrument is that?’ I loved jazz fusion and branched out from there. But Jaco had an edge that far exceeded his jazz persona. He was funk, he was rock, he was soul. And his whole attitude was punk.” He began playing in “a lot of backyard party bands”, playing music by Black Sabbath, Ozzy, Rush, and Led Zeppelin. He went to jazz school when he was 19 with the intention of becoming a studio musician, but he maintained his passion for rock and metal.

Trujillo gained prominence when he replaced Bob Heathcote as the bassist for California crossover thrash band Suicidal Tendencies. Initially billed as “Stymee” on the 1989 album Controlled by Hatred/Feel Like Shit…Déjà Vu, Trujillo remained in the band until the mid-1990s. Concurrent to his work with Suicidal Tendencies, Trujillo was a member of the band’s side project, Infectious Grooves, along with vocalist Mike Muir.

Trujillo joined Metallica on February 24, 2003, two years after Jason Newsted resigned. He had previously met and befriended his future bandmates when Suicidal Tendencies supported Metallica during the Nowhere Else to Roam tour in 1993, and again during the Shit Hits the Sheds Tour one year later. Trujillo received one million dollars from the band as an advance for joining Metallica. His audition and hiring as well as his million dollar payment offer appeared in the documentary film Metallica: Some Kind of Monster. As the current bassist for Metallica, he was inducted into the Rock and Roll Hall of Fame alongside all current members of the band, as well as previous bassists Jason Newsted and Cliff Burton.

With Metallica, Trujillo has primarily been playing Warwick Streamer bass guitars, both 5 and 4-strings. His signature model Streamer bass was released in March 2010. He often plays Fernandes Gravity 5-string basses, particularly a model with a silver finish, blue flame decals, and EMG pickups. In addition to his signature Warwick basses, Zon Guitars produce a signature bass model, the Sonus RT. Prior to Metallica, he was most often seen playing Tobias, ESP and MusicMan basses (all 5-strings), as well as a Fender Precision Bass with Black Label Society and Ozzy Osbourne. Trujillo has been seen in concert playing a Yamaha TRB5-P2 5-string bass, a customized green Rickenbacker 4001/4003 4-string bass modified with EMG pickups, various Nash P-Bass Copy guitars, and both a classic Fender Precision Bass and Fender Jazz Bass. Trujillo is the custodian of Jaco Pastorius’ legendary “Bass Of Doom” (the sunburst fretless 1962 Jazz Bass used by Pastorius on most of his recordings and live appearances). He has performed onstage with Metallica with the instrument.

For amplification, he uses Ampeg amplifiers and cabinets. In 2010, Trujillo collaborated with Jim Dunlop to create his new Icon signature bass strings – these strings are taper-core stainless steel, with a non-tapered B string in gauges 45–130 (5-string).

In 2012, Trujillo produced a documentary about jazz bassist Jaco Pastorius titled Jaco, directed by Stephen Kijak and Paul Marchand. The film was named Official Film of Record Store Day 2014 and was released in November 2014.

Trujillo is married and has a son, Tye, and daughter, Lullah. In April 2017, Tye performed with Korn during their South American tour, filling in for longtime bassist Reginald Arvizu. Tye also plays bass for his new band Suspect208 which also features Slash’s son London Hudson on drums and Scott Weiland’s son Noah Weiland on vocals. Trujillo’s wife, Chloé, has created a pyrography design of the Aztec calendar on one of his basses.