Ally McBeal was a heavily music-oriented show. Vonda Shepard, a virtually unknown musician at the time, was featured continually on the show. Her song "Searchin' My Soul" became the show's theme song. Many of the songs Shepard performed were established hits with lyrics that paralleled the events of the episode, including "Both Sides Now", "Hooked on a Feeling" and "Tell Him". Besides recording background music for the show, Shepard frequently appeared at the ends of episodes as a musician performing at a local piano bar frequented by the main characters. On rare occasions, her character would have conventional dialogue. A portion of "Searchin' My Soul" was played at the beginning of each episode, but remarkably the song was never played in its entirety.

Several of the characters had a musical leitmotif that played when they appeared. John Cage's was "You're the First, the Last, My Everything", Ling Woo's was the Wicked Witch of the West theme from The Wizard of Oz, and Ally McBeal herself picked "Tell Him", when told by a psychiatrist that she needed a theme.

Due to the popularity of the show and Shepard's music, a soundtrack titled Songs from Ally McBeal was released in 1998, as well as a successor soundtrack titled Heart and Soul: New Songs from Ally McBeal in 1999. Two compilation albums from the show featuring Shepard were also released in 2000 and 2001. A Christmas album was also released under the title Ally McBeal: A Very Ally Christmas.[13] The album received positive reviews, and Shephard's version of Kay Starr’s Christmas song "(Everybody's Waitin' For) The Man with the Bag", received considerable airplay during the holiday season.[14]

Other artists featured on the show include Michael Jackson, Barry White, Al Green, Tina Turner, Macy Gray, Gloria Gaynor, Chayanne, Barry Manilow, Anastacia, Elton John, Sting and Mariah Carey. Josh Groban played the role of Malcolm Wyatt in the May 2001 season finale, performing "You're Still You". The series creator, David E. Kelley, was impressed with Groban's performance at The Family Celebration event and based on the audience reaction to Groban's singing, Kelley created a character for him in that finale. The background score for the show was composed by Danny Lux.