The conviction was handed down exactly 41 years to the day that Michael Schwerner, 24, James Chaney, 21 and Andy Goodman, 20, were killed in Philadelphia, Mississippi.
The decision came after two days of deliberations, in which the prosecution reduced its murder charges to manslaughter to break a deadlock among the nine white and three African American jurors who were split 6-6.
Rita Bender, the widow of Mr Schwerner, expressed her disappointment that the jurors “could not bring themselves to acknowledge that these were murders, that they were committed with malice.”
For others though, the judgement has helped turn over one of the United States’ darkest chapters.
“All things considered, I think the compromise of three counts of manslaughter was the best that we can hope for,” said Connie Curry, 70, who met Mr Schwerner in the summer of 1964 in Mississippi.
“It’s good for the soul of this country to have people brought to justice, even 40 or 50 years later,” she added.
On June 21, 1964, the three activists had teamed up to register African American voters.
That night they were ambushed in their car, their bodies found 44 days later beaten and riddled with bullets at a dam.
According to trial witnesses, Killen had rounded up carloads of Klansmen to intercept the three victims.
Claims that Killen told some Klansmen to buy gloves and helped organise a bulldozer to bury the bodies was also included in testimony.
Eighty-year-old Killen, a former Baptist preacher, has denied any part in the deaths.
He told the court he had been attending a wake at a funeral home when the victims were killed.
During the trial, Killen’s lawyers admitted to Killen’s Ku Klux Klan membership for the first time.
But they argued that their client was only a ‘bystander’ in the white supremacist organisation, which was spawned out of the pro-slavery movement in America’s ‘Deep South’.
Killen now faces a penalty of between 20 years and life in prison.
His defence team said they will appeal the conviction because prosecutors changed the charges at the end of the trial.