Police arrested Adlene Hicheur, a 35-year-old researcher studying the universe's birth – the Big Bang – at the European Organisation for Nuclear Research (CERN) in October 2009 after intercepting his emails.
His father embraced him in the Paris court room before he was taken away to serve his term in prison. Hicheur has already spent two and a half years in jail while awaiting trial.
Hicheur admitted at the start of his trial in late March that he was going through a "turbulent" time when he wrote the mails but denied he intended to carry out attacks.
The trial of Hicheur, who was charged with criminal association as part of a terrorist enterprise, began a week after police shot dead Franco-Algerian Mohamed Merah for killing seven people in and around the city of Toulouse.
Prosecutors focused on emails between Hicheur and an alleged Al-Qaeda contact.
Hicheur told the court the emails were written while his "physical and psychological state" was impaired while he was on sick leave for a slipped disc.
Following Hicheur's arrest at his parents' home near CERN, the research institute which lies on the Franco-Swiss border northwest of Geneva, police discovered a trove of Al-Qaeda and Islamist militant literature.
France's DCRI domestic intelligence agency's suspicions were raised after a statement from Al-Qaeda in the Islamic Maghreb (AQIM) was sent to President Nicolas Sarkozy's Elysee Palace in early 2008.
Following the message police carried out surveillance on several email accounts including Hicheur's and his exchanges with Mustapha Debchi, an alleged AQIM representative living in Algeria.
In the emails Hicheur suggested "possible objectives in Europe and particularly in France", mentioning for example a French military base at Cran-Gevrier, close to CERN.
Asked by Debchi if he was "prepared to work in a unit becoming active in France," Hicheur replied: "The answer is of course YES".
Magistrates investigating the case said the exchanges "crossed the line of simple debate of political or religious ideas to enter the sphere of terrorist violence."
They say the accused "knowingly agreed with Mustapha Debchi to set up an operational cell ready to carry out terrorist acts in Europe and in France."