Details of exactly why the 26-year-old actor, who recently won the National Television Award for best newcomer, has been reprimanded are yet to be revealed.
Rumours suggest Best was banned due to bad behaviour.
Best was reportedly called to a crisis meeting with show bosses after breaching the cast’s code of conduct, claim the Daily Star.
"Khali Best has been suspended from EastEnders for three months. We will not comment any further on this matter," said a spokesman.
Fellow cast member Ricky Norwood is still suspended after reports he smoked cannabis on video.
A spokeswoman for the show said at the time: "Ricky would like to apologise to EastEnders viewers for any offence caused and for bringing the show into disrepute."