“Soulef A”, and their two children in Djibouti in mid-December, has been charged with "criminal association with terrorists" and "financing a terrorist enterprise", and held pending a hearing on January 7.
Cherif, 36, who was returned to France in late December and detained, is considered a potential source of valuable information by Western intelligence agencies.
French authorities have been seeking him since he disappeared in 2011 on the final day of his trial in Paris for fighting in Iraq alongside Al-Qaeda in 2004..
He appeared before a French judge on December 27 and was given a new "terrorist conspiracy" charge before returning to prison to serve the five-year sentence from his original trial.
He was close to the brothers who massacred staff members of the French satirical magazine Charlie Hebdo in 2015.
.Cherif, also known as Abou Hamza, was placed on the US blacklist of foreign terrorists in 2015.
Investigators opened a new probe in 2017 into his activities in Yemen, where he joined the senior ranks of the local branch of Al-Qaeda in the Arabian Peninsula (AQAP).
The United States considers AQAP to be the jihadist group's most dangerous branch, with US drone strikes on the outfit increasing since President Donald Trump took office in January 2017.
Soulef A was taken into custody on Sunday upon her arrival in France.