The 34-year-old star also won video of the year, Coca-Cola viewers' choice award and centric award, all for her music video "Formation".
Drake and Bryson Tiller trailed behind with three and two awards, respectively.
Besides the best male hip-hop artist title, Drake nabbed the best group award for his works with Future and best collaboration for his latest hit with Rihanna, "Work", reported Aceshowbiz.
Tiller, meanwhile, was named best male R&B/pop artist and best new artist.
Some actors and athletes were also honored at the ceremony which aired from the Microsoft Theater in Los Angeles.
Taraji P Henson and Michael B Jordan earned the best actress and best actor titles, respectively, while Samuel L Jackson won the lifetime achievement award.
"Straight Outta Compton" won the best movie gong.
In sports categories, tennis player Serena Williams was dubbed Sportswoman of the Year. As for the Sportsman of the Year title, it went to NBA star Stephen Curry.
