If found guilty it could result in the controversial body's main centres being closed down.
The charges, which also include claims of illegally prescribing drugs, were filed by a woman who complained that the Scientologists had allegedly brought about her financial ruin.
She claimed she was psychologically pressured into paying thousands of pounds for lessons, books, drugs and a device called an "electrometre" which the church says can measure a person's mental state.
The case has taken ten years to come to court.
France's professional pharmaceutical association and another plaintiff have also filed for charges.
Scientology is not banned in France.
It is a recognised religion in the United States, where it was founded in 1954 by science-fiction writer L. Ron Hubbard. Followers include Hollywood stars Tom Cruise and John Travolta.
This latest court order refers the church's main structure in France, the ASES-Celebrity Centre, and its bookshop for alleged "organised fraud".
Both could be shut down if convicted, according to judicial sources.
The trial - for which no date has been set - is rare, as most previous cases targeted individuals but not the church itself.
The seven members on trial, including Alain Rosenberg, the manager of the ASES-Celebrity Centre, face a maximum seven year jail term if convicted.
The woman who complained was allegedly approached by Scientologists in a Paris street in 1998. At first she was offered a personality test, then invited to hear the results.
In his order, the judge found that the church had used "personality tests void of scientific value...with the sole aim of selling services or divers products."
The 33-year old was allegedly gradually persuaded to hand over around £25,000 on books, communication and "life healing" lessons, as well as "purification packs".
While claiming to "identify and resolve supposed psychological difficulties or favour personal development," the judge said, the Scientologists' "sole aim" was to "claim their fortune" by "exercising a psychological hold" over her.
The decision to proceed with the case went against a 2006 call by the Paris prosecutor's office for it to be dismissed due to lack of evidence.
A lawyer for the plaintiffs described the judge's decision as "courageous".
The Church of Scientology denounced the ruling, saying it was being "stigmatised" by the courts.
"The special treatment reserved for the Church of Scientology Celebrity Center raises questions about the equality of the justice system and the presumption of innocence," it said in a statement.
