Shepherd was born on an American military base in Okinawa, Japan. His father worked in the Nike missile program and played the guitar. His family moved to Texas, then settled in Kingston, Washington, where Shepherd grew up. Shepherd became interested in music after listening to Johnny Cash on television, sitting as close to the speakers as possible. When Shepherd asked his father for a guitar, his father complied only after insisting he must learn every chord in a large book with nothing but a guitar neck. Shepherd did so—with help from his cousin Ralph "Tony" McMullen—and his father bought him his first guitar.
Shepherd played in numerous punk-rock bands with friends as a teenager like March of Crimes, Mind Circus and 600 School, meeting future musicians such as Stone Gossard, Krist Novoselic and Matt Cameron. After graduating from high school, he worked as a carpenter and a laborer, and while playing in Tic Dolly Row with drummer friend Chad Channing, introduced him to Novoselic, who went on to bring Channing into his band Nirvana. Shepherd would later travel with Nirvana on a tour leading up to the release of Nevermind, being a nominal second guitarist but not playing on stage.
Shepherd was a fan of Soundgarden ever since their early days as a three-piece. Once bassist Hiro Yamamoto left in 1989, Shepherd auditioned to replace him even as his primary instrument was the guitar. The band members liked Shepherd and his attitude, but given he did not know how to play the songs, they eventually picked bassist Jason Everman. Following the closure of the Louder Than Love tour in 1990, Everman was fired, and the band contacted Shepherd to see if he could join the band. His introduction was deemed by Soundgarden as helpful towards their musical evolution, bringing his own compositions that showed a new style, and guitarist Kim Thayil adding that Shepherd gave "a creative and emotional punch". In addition to his role as bass player, Shepherd's role as a singer and songwriter increased during his tenure with Soundgarden. On his first recording with the band, the studio album Badmotorfinger, Shepherd took part in writing the following songs: "Slaves & Bulldozers" (music, co-written), "Jesus Christ Pose" (music, co-written), "Face Pollution" (music), and "Somewhere" (music and lyrics). Shepherd also introduced some of the now signature alternate tunings to the band, such as in the singles "The Day I Tried To Live", "My Wave", "Pretty Noose", and "Burden in My Hand".
In 1993, Shepherd and Soundgarden drummer Matt Cameron formed a side-project band called Hater with John McBain of Monster Magnet. Shepherd sang vocals and played guitar in Hater, in addition to writing several songs on the band's first release, a self-titled album. A second album called The 2nd was recorded in 1995 after Superunknown tour's end, but was not released until 2005, ten years later.
In 1994, Soundgarden released Superunknown, which featured Shepherd compositions "Half" and "Head Down". The latter of which was heavily influenced by The Beatles and was written after experimenting with mic placement on his Gibson L-50, picking up the guitar and strumming it to find he liked the wildly out of tune sound, making up the song's composition on the spot. "Half" was marked by an Indian flavor and was the first song on a Soundgarden album for which Shepherd sang lead vocals. Shepherd has said that "Half" was a song he wrote in case his daughter ever wanted to learn guitar.
In 1996, Soundgarden released Down on the Upside, in which six of the sixteen album tracks were lyrically and/or musically composed by Shepherd. The tracks were: "Zero Chance" (music), "Dusty" (music), "Ty Cobb" (music), "Never Named" (music) "Switch Opens" (music) and "An Unkind" (music and lyrics). Shepherd once said he penned the music for "Never Named" at the age of sixteen. "Ty Cobb" was the first song Shepherd wrote that was made a single.
The Down on the Upside tour ended on February 9, 1997 in Honolulu, with an acrimonious meltdown started by Shepherd. With the band in a bad mood and facing technical problems in their performance, Shepherd eventually got so frustrated - "I’d had it up to here with my equipment dying. So I wasn’t going to stand onstage and fake what I was playing." - he smashed his bass during "Blow Up The Outside World," gave the audience the finger and left the stage. He then started a heated argument with Thayil backstage that nearly escalated into a fistfight, leading to only Cornell and Cameron returning for the encore. Two months later, Soundgarden announced it was breaking up, citing dissatisfaction and artistic differences.
Shepherd said that he was the one most affected by Soundgarden's breakup: "my fianceé broke up with me; and then I broke three ribs. I got addicted to pain pills, drank a ton, and wound up OD’ing on morphine. I was laid out in my house for five days, and no one knew it. It was a fucking horrible time — this total rock’n’roll cliché."
Hater also disbanded, but he, Cameron, and McBain would go on to form Wellwater Conspiracy with several other artists. Shepherd was the lead vocalist on the first Wellwater Conspiracy album, Declaration of Conformity. In 1998, he quit Wellwater Conspiracy for unknown reasons. Matt Cameron took over lead vocals.
In the years after the split, Shepherd participated in some of Josh Homme's Desert Sessions collaboration (Volumes 1 & 2), on which he played bass and guitar, and played bass with Mark Lanegan (in the 1999 album I'll Take Care of You and 2002's Field Songs, where he even wrote co-wrote the song "Blues For D"), and Tony Iommi (2000's Iommi). In 2005, Shepherd formed the shortly lived band Unkmongoni and released the second Hater album, The 2nd.
In 2008, following the sale of the warehouse Soundgarden's equipment was being stored in, Shepherd was robbed of all his equipment including guitars, basses, and amplifiers collected and used through Soundgarden's career, and 2 records he had completed. Following the incident, a downtrodden Shepherd decided to quit music altogether and became a carpenter's assistant until he was eventually coerced into making his solo record In Deep Owl and reuniting with Soundgarden shortly thereafter.
In an August 2010 feature about the Soundgarden reunion with Spin, Shepherd stated that before reuniting he was "totally broke" and was sleeping on friends' couches. Shepherd has since downplayed the statement, stating that he was only "sleeping on couches in studios when I was recording my solo album", preferring to stay in Seattle rather than go back home to Bainbridge Island.
On January 1, 2010, Chris Cornell confirmed that Soundgarden would reunite, with Shepherd playing as their bassist again. The band played its first show in 13 years on April 16, 2010 at Seattle's Showbox theater under the anagram Nudedragons.
The group released the compilation album Telephantasm in September 2010, followed by King Animal in November 2012, their first studio album since 1996. Shepherd's contributions included two songs which he had written years before and recorded in the eventually stolen demos, "Taree" and "Attrition", and two collaborations with Cornell, "Been Away Too Long" and "Rowing".
The band continued to tour frequently, arranging time around Matt Cameron's schedule in Pearl Jam, and Chris Cornell's acoustic tours. In 2014 the band released a reissue of their 1994 album Superunknown as part of its twentieth anniversary and has toured with drummer Matt Chamberlain filling in for Cameron. On May 17, 2017, Chris Cornell was found dead in his hotel room, cancelling the rest of their tour.
In the summer of 2010, Shepherd finished recording his latest solo project. He began writing the record in 2009. It started out as an acoustic project, before morphing into a very electrified concept album in the end. Shepherd originally intended for the songs to be just voice and acoustic guitar, but soon Matt Cameron and Matt Chamberlain offered up their services on drums. The album was recorded by Dave French, at a few different studios including KAOS in Georgetown, and The Studio With No Name in Interbay. The album was finished, mixed/mastered at Robert Lang Studios by Adam Kasper and contains a recording of frog ribbits.
On June 25, 2013, Shepherd announced he would be releasing the solo album entitled In Deep Owl on August 27, 2013 under the name HBS. Shepherd premiered the first single "Baron Robber" on Spin. The drummer on "Baron Robber" is Joseph Braley who also drums for Seattle-based bands MASZER, The Mother's Anger and the band Reignwolf. Featured musicians include:
Shepherd has two children, a daughter Ione, and a son named Noah. He currently resides on Bainbridge Island, Washington. Shepherd is also the partial owner of an upscale Seattle bar called Hazelwood.
Given Shepherd started playing bass trying to replace Hiro Yamamoto, he considers his Soundgarden predecessor a major influence, particularly as Yamamoto differed from bassists "relegated to a role of following along", even if his bass "was mixed so damn quietly on the recordings that I could never hear him well enough to develop a deep understanding of his fluidity or his textures." Shepherd followed a fingerstyle playing based on Yamamoto, Chuck Dukowski from Black Flag, and Mike Watt, and listened to Charles Mingus "because I wanted to learn how to play some dirty, weird shit." Certain songs have Shepherd using a pick to provide "different textures". Shepherd considers that he approaches guitars "like a horn section", split between rhythm and lead, while "Bass is more fluid; you're a lot more free to do stuff because it's a song within a song". His preference is to play the bass along to the vocals, as "it helps to harmonize."
As a singer, Shepherd described himself as "trying to find out who I sound like, not like someone else." Composing is usually done by Shepherd on the guitar, given all other Soundgarden members play that instrument. Bass-minded tracks such as “Switch Opens” are rare because, as he explained "you don’t want to write a whole wandering bass line wondering what the drum beat and the guitar chords are going to be."
Ben used a mixture of Ampeg and Mesa for recording, but led more to the Mesa's live in Soundgarden.
Shepherd uses GHS Bass Boomers Heavy gauge (50-115), and likes them to be as worn as possible, oftentimes leaving them on for years until they eventually break. Shepherd has used the Leo Quan Badass Bass II bridge and continues to use them on almost all his Fenders. He as of late has also equipped his basses with stereo output jacks for durability.