In 1558, the French troops led by Maréchal de Thermes invaded the city and burnt the church.

The re-construction of the church started in 1559 under the supervision of prime contractor Jean de Renneville and ended in 1567.

[4][3] The sanctuary was enlarged to the east, the main nave was elevated and the side aisles were re-built with chapels.

In 1782, extension works were made by architect Victor Louis on the behalf of intendant de Calonne to cope with the population growth.

The Gothic Revival project of architect Adolphe Van Moë [fr] was selected.

[3][5] The first stone was laid on April 11, 1887, and the new façade was ended in 1889 by the city architect Jules Lecoq [fr].

After long restoration works funded by the war damage compensation (dommages de guerre), the church was re-opened.

[6] The sacristy of Saint-Éloi hosts the remains of the corsair Jean-Bart (1650–1702) who became famous for the Battle of Texel.