Killen, 80, had been portrayed by prosecutors as a Ku Klux Klan leader who recruited a mob to kill Michael Schwerner, Andrew Goodman and James Chaney exactly 41 years ago, on 21 June 1964.
The killings in Neshoba County were dramatised in the 1988 movie Mississippi Burning.
The jury found Killen guilty on three counts of felony manslaughter but not guilty of the more serious charge of murder.
Circuit Judge Marcus Gordon ordered him to be held at the Neshoba County Sheriff's office pending sentencing on Thursday.
Killen, who faces up to 20 years in prison, showed no visible emotion as the verdict was read.
He had an oxygen tube in his nose and bailiffs wheeled him away in the wheelchair he has used since breaking both legs in a logging accident in March.
The trial in the small Mississippi town of Philadelphia, the latest in a string of prosecutions in recent years from civil rights era killings in the south, evoked memories of the violent racial conflicts of four decades ago.
Killen, a sawmill operator and Baptist preacher, did not testify.
He was accused of murdering Schwerner and Goodman, white New Yorkers, and Chaney, a black Mississippian, who were helping black Americans in Mississippi register to vote during the 1964 Freedom Summer civil rights campaign.
If convicted of murder he would have faced life in prison.
Abducted and shot
The three victims, all in their 20s, were abducted and shot by a group of Klansmen on a remote road outside the eastern Mississippi town. Their bodies were found weeks later in an earthen dam.
"I hope that this conviction helps to shed some light on what has happened in this state. I see it as a very important first step," Rita Bender, widow of Michael Schwerner, said.
Killen was among a group of men tried in 1967 for violating the civil rights of Schwerner, Goodman and Chaney.
Seven co-defendants were convicted by the all-white jury and served up to six years in prison but Killen's trial ended in a hung jury after a lone holdout said she could never convict a preacher.