RKellyTV and RKellyVevo were taken down on Tuesday, YouTube confirmed.
"Egregious actions committed by R. Kelly warrant penalties beyond standard enforcement measures due to a potential to cause widespread harm," YouTube VP of legal Nicole Alston said in a statement obtained by Bloomberg. "Ultimately we are taking this action to protect our users similar to other platforms."
The catalog of his music will however be available on YouTube Music, YouTube's audio-streaming service, and the videos uploaded by other YouTube users will continue to be available.
Kelly's music has largely disappeared from radio but is still available on streaming platforms. His hit record "I Believe I Can Fly" was for years a popular choice at graduation ceremonies.
The musician was convicted by a federal jury in September in his sex trafficking trial, where prosecutors accused the singer of exploiting his stardom over a quarter-century to lure women and underage girls into his orbit for sex.
Kelly faces a mandatory minimum of 10 years behind bars, and could face up to life in prison at his May 4, 2022, sentencing.
The singer, whose full name is Robert Sylvester Kelly, is one of the most prominent people tried on sex charges during the #MeToo movement, which amplified accusations that had dogged him since the early 2000s.
Reuters contributed to this report.