He had been tweeting hints that he has left the station, confirming he will no longer be on the radio Monday morning.
The broadcaster had been presenting the breakfast show on BBC Three Counties for the last three years.
A BBC spokesperson told Premier that: "Iain Lee will no longer be presenting his shows on the station but we want to take this opportunity to thank him and wish him well for the future."
Premier has asked the BBC the nature of Mr Lee's departure and is awaiting a response.
November 14, 2015
A tweet from Iain read: "Thanks everyone. I've enjoyed every second of it. See you sometime in the future."
Iain apologised most recently for the way he conducted an interview with a Christian Concern campaigner.
The BBC also apologised for his interview about the Bible's teaching on homosexuality in which a Christian woman was labelled a bigot.
Libby Powell, from campaign group Christian Concern, appeared on BBC Three Counties Radio earlier this month
She was discussing the case of Revd Barry Trayhorn, a prison worker taking his employer to a tribunal amid claims he was forced to resign for reading a Bible verse about homosexuality.
Mr Lee asked if Revd Trayhorn would embrace gay people and when told by Ms Powell that he would, he replied "bit gay".
The BBC admitted the language the presenter used, and the tone in which he conducted the interview, was "at several points inappropriate".
I'm blocking so many people. I'll make it easy. If you think gays and lesbians are sinners, please unfollow me.— Iain Lee (@iainlee) November 13, 2015
A statement from senior editorial staff said: "The BBC - and Iain Lee himself - wish to apologise for any offence that may have been caused."
Iain Lee also apologised on air and said: "Last week I interviewed the Revd Barry Trayhorn and solicitor Libby Powell about their understanding of biblical teaching on homosexuality.
"I want to make it clear that I apologise for any offence that may have been caused over the way I conducted the interviews."
Sorry for any offensive my interview may have caused. I think this article says all that needs to be said. https://t.co/lT1L1RZQMF— Iain Lee (@iainlee) November 12, 2015
Christian Concern had labelled the interview "intolerant" and asked its supporters to complain.