Army Spc. Agustin Aguayo, 34, turned himself in around 6 p.m. at Fort Irwin, an Army base in the Mojave Desert northeast of Los Angeles, said Army spokesman Ken Drylie.
"It is the right thing to do," said Aguayo at a news conference in Los Angeles hours before going to the base. "I'm not a deserter or a coward."
Aguayo said he expected to face a court martial and some jail time.
"It's something I can live with," he said. "Something I can't live with is being a participant of war anymore."
Aguayo has unsuccessfully fought the Pentagon for more than two years to be declared a conscientious objector and win a discharge.
Aguayo, a U.S. citizen who was born in Guadalajara, Mexico, said he was not anti-war when he enlisted in 2002. But his military experiences changed his mind. He applied for conscientious objector status in February 2004 before he was sent overseas.
He served a year as a combat medic in Tikrit, Iraq, in 2004 after the military turned down his request.
He then jumped out of a window of his base housing in Germany on Sept. 2 rather than be forced to ship out for a second tour with the 1st Battalion, 18th Infantry Regiment.
"I have come to believe that it is wrong to destroy life, that it is wrong to use war, that it is immoral, and I can no longer go down this path," Aguayo said.
After being taken into custody, Aguayo will be sent to either Fort Sill in Oklahoma, or Schweinfurt, Germany, said John Wagstaffe, an Army spokesman at Fort Irwin. Army officials would then decide whether to court martial him, said Wagstaffe.
Aguayo likely will be charged with being AWOL and with a separate charge of missing movement because he didn't ship out to Iraq with his unit, said James Klimaski, one of Aguayo's Washington attorneys.
Other soldiers who went AWOL and claimed they were conscientious objectors have been sentenced to between a couple of months to two years in confinement and given bad conduct discharges, Klimaski said.
Last year, Aguayo sued in federal court in Washington to overturn the military's rejection of his conscientious objector bid. He lost the court case but has appealed the decision. Arguments are scheduled for November. If Aguayo wins his lawsuit on appeal, that would overturn any court-martial decision, Klimaski said.