Sid Ahmed Ghlam, 24, had been taken into police custody Sunday after he accidentally shot himself in the leg and called for emergency medical services.
Police then found an arsenal of weapons in the computer science student’s car and apartment, as well as plans to attack at least one church south of Paris and documents in Arabic mentioning the Islamic State armed group and Al-Qaeda.
Police also linked Ghlam's DNA to the murder of a 32-year-old woman who was found shot dead in the passenger seat of her car on Sunday.
Ghlam had previously drawn the attention of French intelligence agents over his postings on social media expressing his desire to join jihadists fighting in Syria in 2014. Officials also made checks earlier this year when he travelled to Turkey, but found nothing suspicious, according to Interior Minister Bernard Cazeneuve.
Investigators say Ghlam was not acting alone.
A police source told French news agency AFP that the suspect had an unusual profile and appeared to be "remote-controlled from afar by one or more mysterious men", likely in Syria, who ordered him to target churches.
Meanwhile, Paris prosecutors have released a 25-year-old woman taken into custody Wednesday for questioning after investigators discovered encrypted electronic communications between her and Ghlam.
Cazeneuve has ordered authorities to step up security around churches.
France has been on maximum alert following the January terror attacks on the offices of the Charlie Hebdo satirical weekly and a Jewish food shop, in which 17 people were killed.