"I am innocent," The 27-year-old mother of four told the judge in French.
"My husband duped me and then threatened to leave with the children" unless she followed him to Iraq, where he planned on joining IS, she said.
Three of her children have been sent back to France.
Boughedir was captured in the northern Iraqi city of Mosul, the capital of IS's self-declared "caliphate", when it fell to government forces in 2017.
She was sentenced last February to seven months in prison for illegal entry into the country and was set to be deported back to France, but another court ordered her retrial under Iraq's anti-terrorist law on charges that could have meant a death sentence.
On Saturday her French lawyers, who travelled to Baghdad for the trial, accused French Interior Minister Jean-Yves Le Drian of "unacceptable interference" in her case after he told the LCI TV station that she was a "terrorist".
"When you got to Mosul in 2016 it's to fight and she is being judged at the scene of these crimes," he said. "That's normal logic."
But he confirmed France's opposition to the death penalty.
"Nobody can doubt that in these circumstances if a stiff sentence is passed tomorrow it would be immediately related to the unacceptable interference that you have been responsible for," William Bourdon, Martin Pradel and Vincent Brengarth said in a letter.
Boughedir's Iraqi lawyer had not been able to consult the documentation on her case or visit her in prison, they said.
They accused Le Drian of wanting to prevent her being sent back to France, despite the fact that she is wanted for alleged terrorist plotting here.
Faced with dozens of foreign women who went to IS-held territory, the Baghdad court has sentenced many of them after hearings that have been as short as 10 minutes.
Another Frenchwoman, 29-year-old Djamila Boutoutaou, was also given a life sentence in April, despite her claim that she had been tricked by her husband.