In November last year, Libby Powell, from campaign group Christian Concern, appeared on the breakfast show defending 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.
During the interview she was called a bigot after she said homosexuality was a sin.
Iain Lee said Revd Trayhorn was "obnoxious" and "poisonous" and said his views, and Ms Powell's were homophobic.
When Ms Powell said homophobia was a fear, Mr Lee said it was a "cute answer" but homophobia was a "hatred of gays".
He asked if Revd Trayhorn would embrace gay people and was told by Ms Powell that he would.
"Bit gay," replied Mr Lee.
The BBC apologised soon after the broadcast stating the language the presenter used, and the tone in which he conducted the interview, was "at several points inappropriate".
The BBC Trust, which acts as the final stage of the BBC complaints process, has now ruled on the interview, and another with Revd Trayhorn, stating Mr Lee did not show due impartiality.
It said: "[The trustees] considered that in both interviews, the interviewees were not treated with respect but instead faced significant personal criticism and challenge and that, overall, the tone of the interviews was inappropriate.
"The Trustees considered that the presenter should have been able to robustly and properly challenge the interviewees without recourse to personal attack and without taking a personal position on it.
"They noted that a final interviewee from the Gay and Lesbian Christian Movement was able to challenge the views of the two previous interviewees in a manner that was measured and productive."
The Trust's report states that Iain Lee stands by the interviews in terms of their content and tone and the only part he felt was inappropriate was his comment which referred to some Christians behaving in a "horrible, patronising, superior way" which he wished to apologise for.
Genuinely,I'm flabbergasted. The report contains examples of where I was wrong. Apart from 1 line, I kept replying 'what's wrong with that?'
— Iain Lee (@iainlee) 8 March 2016
Honestly, I don't know what I did wrong.
— Iain Lee (@iainlee) 8 March 2016
Iain Lee left the BBC shortly after the interviews were broadcast.
He is now presenting on the new digital station talkRADIO.