Kelly is up for the Ashford & Simpson songwriter's award and album of the year for "Write Me Back," bringing his career total to 21 nominations.
Usher leads this year's awards with five nominations. Estelle, Nas, Trey Songz and John Legend are also multiple nominees.
Whitney Houston is nominated for best gospel inspirational performance, and Amy Winehouse is nominated for best international performance. New Edition will receive a lifetime achievement award.
The Soul Train Awards, hosted by Cedric the Entertainer, will air Nov. 25 on BET and Centric.
Usher, meanwhile, recently signed on as a coach for the upcoming season of NBC's "The Voice."