Keys, who won five Grammys in February, won in the best R&B/soul new artist category for her hit Fallin', while her album Songs In A Minor took the best R&B/soul female album award.
Keys was also named female entertainer of the year.
The Isley Brothers, whose career started in the late 1950s, also won three awards.
The surviving brothers, Ronald, Rudolph, Ernie and Marvin were honoured for the best R&B/soul single for Contagious, and the best group album for Eternal.
The group, whose first hit was Shout in 1959 and who recorded the original Twist And Shout, were also named male entertainers of the year.
The late R&B singer Aaliyah won the best female R&B/soul single award for Rock the Boat.
Oustanding
She died in a plane crash in August, shortly after completing a video for the song in the Bahamas.
Veteran soul group the O'Jays won the Quincy Jones award for outstanding career achievement.
Usher won the best male R&B/soul album award for 8701, while rapper Jay-Z won in the rap album category for The Blueprint.
Missy "Misdemeanor" Elliot's Get Ur Freak On won the best video award.
The awards, at the Los Angeles Sports Arena, were hosted by TV talk show host Arsenio Hall, and R&B singers Faith Evans and Yolanda Adams.