Speaking at a mosque in the city on Friday - four days after the suicide bombing by Salman Abedi, which killed 22 people - he said murderous extremists did not represent Islam.
Mr Farron said: "I am a committed Christian, but, do you know what? There is an organisation in America that has killed a minimum of 4,000 people, probably ten or 20 times more than that over the last century and a half, it calls itself a Christian organisation - it is the Klu Klux Klan.
"They do not speak for me; they do not speak for Christians."
The comments come after a recent period of intense scrutiny surrounding Mr Farron's personal beliefs. Earlier this month, he voiced his support for abortion after The Guardian said it had come across an interview of his saying terminations were "wrong."
He also recently denied believing that homosexuality was a sin, after his failure to directly address the issue attracted a wave of criticism.
Speaking in nearby Warrington earlier on Friday, Mr Farron also responded to the Labour Party's leader Jeremy Corbyn who on Friday sought to link attacks in the UK with the country's involvement in the "war on terror".
Mr Farron said: "I think the choice of today to make a political statement and to attach blame, in some way, to someone other than the terrorist, I think that's unfortunate."
Mr Corbyn defended his comments while on the election campaign trail on Saturday, saying: "The attack was horrendous, awful and was murder.
"What I said was 'we have to be serious about the situation that exists in Libya and other countries and a sensible government would also be looking at the international situation.
"Ungoverned spaces in Libya are a danger to all of us."
Abedi was the child of Libyan parents.
Meanwhile, Prime Minister Theresa May announced on Saturday the UK terror threat level has been reduced from "critical" to "severe" - meaning an attack is no longer considered imminent, but highly likely.
She said: "From midnight on Monday onwards there will be a well-planned and gradual withdrawal of members of the armed forces who will return to normal duties."