The R&B crooner received a best male R&B-soul album nod for "TP.3 Reloaded," while his song "Trapped in the Closet (Chapter 1 of 5)" garnered nominations for best male R&B-soul single and best R&B-soul or rap music video.
Kelly is also the first recipient of the Stevie Wonder award for outstanding career achievements in song writing. Wonder will present the honor at a March 4 ceremony.
Nine other recording artists reaped two nominations each, including rap quartet the Black Eyed Peas and solo stars Keyshia Cole, Missy Elliott, Gwen Stefani, Charlie Wilson, Bobby Valentino, John Legend, Mariah Carey and Kanye West.
Legend, Carey and West are all Grammy favorites, with eight nominations each. Kelly has one, for best long form music video.
Kelly, dogged by continuing child pornography charges, earned favorite soul-R&B artist honors at the American Music Awards in November.
Other honorees at the 20th annual Soul Train Music Awards include Academy Award winner Jamie Foxx and chart-toppers Destiny's Child, who will be recognized for outstanding career achievements by legendary musician Quincy Jones.
Legend will be presented with the 2006 Sammy Davis Jr. Entertainer of the Year award.
The Soul Train Music Awards, started by the syndicated music show "Soul Train," celebrate artists in R&B, hip-hop, rap and gospel music. The 2006 honors will be presented at the Pasadena Civic Auditorium.
The awards are determined by a group of radio station professionals, talent managers and performers.
Complete list of nominees:
R&B-soul single, female: "We Belong Together," Mariah Carey; "I Should Have Cheated," Keyshia Cole; "Unbreakable," Alicia Keys; "Hollaback Girl," Gwen Stefani.
R&B-soul single, male: "Trapped in the Closet (Chapter 1 of 5)," R. Kelly; "Ordinary People," John Legend; "Slow Down," Bobby Valentino; "Charlie, Last Name Wilson," Charlie Wilson.
R&B-soul single, group, band or duo: "Cater 2 U," Destiny's Child; "Supastar," Floetry featuring Common; "Turning' Me On," Nina Sky featuring Pitbull; "Don't Cha," The Pussycat Dolls featuring Busta Rhymes.
R&B-soul album, female: "The Emancipation of Mimi," Mariah Carey; "The Way It Is," Keyshia Cole; "The First Lady," Faith Evans; "Free Yourself," Fantasia.
R&B-soul album, male: "Soulife," Anthony Hamilton; "TP.3 Reloaded," R. Kelly; "Get Lifted," John Legend; "Charlie, Last Name Wilson," Charlie Wilson.
R&B-soul album, group, band or duo: "Pleasure & Pain," 112; "Monkey Business," Black Eyed Peas; "Illumination," Earth, Wind & Fire; "Livin' the Luxury Brown," Mint Condition.
R&B-soul or rap new artist: "Run It," Chris Brown; "Music," Leela James; "Must Be Nice," Lyfe Jennings; "Slow R&B Down," Bobby Valentino.
R&B-soul or rap music video: "Testify," Common; "Lose Control," Missy Elliott featuring Ciara and Fat Man Scoop; "Trapped in the Closet (Chapter 1 of 5)," R. Kelly; "Gold Digger," Kanye West featuring Jamie Foxx.
R&B-soul or rap dance cut: "My Humps," Black Eyed Peas; "Lose Control," Missy Elliott featuring Ciara and Fat Man Scoop; "Hollaback Girl," Gwen Stefani; "Gold Digger," Kanye West.
Gospel album: "One Church," Kurt Carr Project; "Hero," Kirk Franklin; "Psalms, Hymns & Spiritual Songs," Donnie McClurkin, "Purified," CeCe Winans.