The church was suppressed in 1790 during the French Revolution and turned over the next year for use as the first building dedicated to Protestant worship in the history of Paris, a role in which it continued until its demolition in 1811 to make way for Napoleon's expansion of the Louvre.

After Robert's death, his wife, Agnès de Baudemont, obtained confirmation of the foundation of the church from Pope Clement III in 1189.

In 1428, John VI, Duke of Brittany endowed more prebends for the church by donating the adjoining hotel, La Petite Bretagne, on the condition that the canons pray for his family.

This accident led to the union of the chapter with that of the neighboring Saint-Nicolas-du-Louvre, which had also been founded by Robert of Dreux and had at various times previously been united with Saint-Thomas, and the rededication of the reconstructed church to Saint Louis in 1744.

[2] When Cardinal Fleury, the tutor and chief minister of Louis XV, died in 1743 the king decided that his mausoleum would be placed in Saint-Louis-du-Louvre.

A competition was held for the commission to create the tomb, a landmark event in the history of 18th century French sculpture due to its solicitation of public input.

Models for the tomb were offered by Nicolas-Sébastien Adam, Edmé Bouchardon, Charles-François Ladette, Jean-Baptiste II Lemoyne, and Jean-Joseph Vinache.

Bouchardon won the competition though ultimately Lemoyne was given the commission by the family of Cardinal Fleury and the tomb remained unfinished at the time of the church's suppression.

[7] This inaugurated a long period of persecution for French Protestants, though some in Paris were able to worship in the chapels of the Dutch and Swedish embassies.

[8] The Edict of Tolerance in 1787 gave Protestants legal status and a congregation was formed under the pastorship of Paul-Henri Marron, who had been serving as the chaplain at the Dutch embassy.

[6] Marron was once more arrested in June 1794 for continuing to marry and baptize in secret after Christian practice had been banned by Robespierre in favor of the Cult of the Supreme Being.