The man, already held and released by police last week, was indicted “on charges of destruction and damage by fire” of the gothic cathedral of Nantes, the public prosecutor for the western city said.
The fire broke out on July 18, hours after the volunteer altar server had closed up the building for the night.
Prosecutors launched an arson investigation into the blaze, which they said appeared to have hit three different parts of the Cathedral of St Peter and St Paul.
Police investigating the incident had arrested the 39-year-old Rwandan national and then released him last week.
His lawyer said at the time there was nothing directly linking his client to the fire.
This file photo taken on July 18, 2020 shows the remains of the burnt organ after falling from the 1st floor during a fire inside the Saint-Pierre-et-Saint-Paul Cathedral in Nantes.AFP
But following developments in the inquiry, the man was rearrested on Saturday and later appeared before a judge in the city, prosecutor Pierre Sennes said in a statement.
The blaze came just 15 months after a devastating fire tore through the Notre-Dame cathedral in Paris.
It destroyed the Nantes congregation's famed organ, which dated from 1621 and had survived the French revolution and World War II bombardment.
Also lost were priceless artefacts and paintings — including a work by 19th-century artist Hippolyte Flandrin — and stained glass windows which contained remnants of 16th-century glass.