In 1997, Whalum jumped labels to sign with Warner Bros. His first solo album on Warner's tab, Colors, was released that same year, and perhaps more than any other album, showed Whalum's ability to synthesize music from a variety of sources to produce a fusion of pop, jazz, and R&B. The following year, Gospel According to Jazz, Chapter 1 exhibited his ability to return to the music of his childhood stylistically, while also pursuing the kind of spiritual depth that has a long history in jazz, echoing artists like John Coltrane in taking advantage of the saxophone's unique expressive qualities. The decade also brought Whalum an amazingly diverse series of session and touring jobs, working with artists like Whitney Houston, Babyface, Yolanda Adams, Take 6, Bebe & Cece Winans, Barbra Streisand, Edwin Hawkins, Quincy Jones, Kevin Mahogany, Al Green, and Luther Vandross. In addition to his solo albums, Whalum worked on a number of film scores, including those for The Prince of Tides, Boyz in the Hood, Grand Canyon, and Cousins. His sax solo was featured on Whitney Houston's wildly popular single "I Will Always Love You," on the soundtrack for The Bodyguard.

The fan base that Whalum had been building throughout the '80s and '90s exploded with his 1998 release, For You, which spent nearly two years at the top of the Billboard Contemporary Jazz Chart and yielded four Top Ten NAC hits. His self-produced album, 2000's Hymns in the Garden, made a much quieter impact but was critically acclaimed, even earning Whalum a second Grammy nomination. Also in 2000, Whalum recorded again for Warner Bros. and released Unconditional, his third album for the label. Unconditional returned to the contemporary jazz style that had marked his early releases, with a few unexpected covers, including versions of Macy Gray's "I Try" and *NSYNC's "God Must Have Spent a Little More Time on You." "Can't Stop the Rain," a song written and sung by Shai, is the only other song on the album not composed by Whalum. Since 2001, Whalum has released four studio albums, including his second volume of gospel songs, The Gospel According to Jazz: Chapter 2, and Kirk Whalum Performs the Babyface Songbook, released on Rendezvous Music in 2005. In 2008, Whalum released Promises Made, a benefit album for the Millennium Project dedicated to the relief of hunger, disease prevention, and economic development in Africa. In 2010, Whalum issued The Gospel According to Jazz: Chapter III. This volume included appearances by George Duke, Lalah Hathaway, Bishop T.D. Jakes, and Kevin Whalum, among others. Whalum was made President and CEO of the Stax Museum of American Soul Music later in the year, and in August, he released Everything Is Everything: The Music of Donny Hathaway, his second album of the year on Rendezvous Music.