The man had talked about plans to attack the Part-Dieu district of the city in central France, an area with a railway station and large shopping centre, local newspaper Le Progres reported.
Investigators, who arrested the man on Monday, said they had no evidence that the Calais native had a "concrete plan" to attack, however he reportedly had "worrying" links to other suspected radicals.
These included a Frenchman suspected of acting as a 'recruiter' for terrorist networks and being behind the murder of a French priest in the Normandy town Saint-Etienne-du-Rouvray.
The 25-year-old, described as unstable, had been convicted of numerous "malicious phone calls" and false terrorist alerts in 2014, and had converted to Islam while in prison, 20 Minutes reported.
Investigators have described him as a "very troubled" individual, and other residents of the building where he lived told local media of the man's strange behaviour, for example talking to himself alone in the street.
Interior Minister Bernard Cazeneuve announced on Tuesday that seven people with links to terrorist networks had been arrested in August, three of whom apparently had "established plans" to attack.
France remains on high alert following two attacks in July; the Bastille Day attack in Nice, which saw a 31-year-old kill 85 after driving into crowds with a 19-tonne truck, and the murder of the priest just under two weeks later.