The 33-year-old man, referred to as Ahmed H, is accused of having participated in the June 2014 capture and execution of an estimated 1,700 young army recruits, most of them Shia-Muslims, from the Speicher military camp to the north of Tikrit.
Ahmed H was arrested in March and indicted days later.
He denies any involvement.
The Paris prosecutor said the suspect was placed in pre-trial detention and faces a range of charges including "killings in connection with a terrorist group" and "war crimes".
Having arrived in France in the summer of 2016, Ahmed H obtained refugee status a year later and was given a 10-year resident card.
Shortly after being granted his refugee status, Ahmed H was identified and followed by intelligence services, who then notified judicial authorities.