R Kelly's removal comes under the new "Hate Content & Hateful Conduct" policy, which is created to "be consistent with our distinct roles in music and media".
Kelly's music will still be available to stream on the site, but Spotify will no longer promote it through playlists like RapCaviar.
"We do not censor content material due to an artist's or creator's habits, however we wish our editorial selections - what we select to programme - to mirror our values".
The statement continues: "We've also thought long and hard about how to handle content that is not hate content itself, but is principally made by artists or other creators who have demonstrated hateful conduct personally".
Kelly, who has repeatedly denied the allegations, responded by suggesting that the claims against him amounted to "lynching."
This post was updated on May 10 to include additional information regarding XXXTentacion.
According to a BuzzFeed investigation published last July, Kelly is also accused of holding six women in virtual slavery at his homes in Chicago and Atlanta, with power over their clothing, diet and sexual encounters.
Jonathan Prince, head of Spotify's content and marketplace policy, elaborated on the company's decision to Billboard.
The post concludes: 'This is our first iteration of this new policy.
The move comes just weeks after a Time's Up initiative kicked off a public pressure campaign to boycott R Kelly's music and live shows following numerous allegations of the artist's recent and historical abuses against women.
No other artists have yet been affected by the policy.
Official Spotify playlists are labelled "by Spotify". And there are a multitude of songs from artists in different genres that could be construed as hateful. This included the Southern Poverty Law Center, the Anti-Defamation League, Color Of Change, Showing Up for Racial Justice (SURJ), GLAAD, Muslim Advocates and the International Network Against Cyber Hate. And we listen to our users - if you think something is hate content, please let us know and we will review it carefully against our policy.