The present organ at Saint Étienne-du-Mont, completed in 1956, was not simply one installation among many by its builder. Those involved in the effort clearly believed, in the beginning, that it would be a routine enterprise. But the design, construction, and installation of the instrument became a complicated saga of so many trials, missteps, and disputes that it took eighteen years to complete.

Very little is known about the organs at Saint Étienne-du-Mont prior to the seventeenth century, and their succeeding history is complex. It is known that the church had an organ in 1517, and that Jehan d’Argillières, an organist and builder of organs and harpsichords, did repairs on it in 1573–75, while the new church was still under construction and while Nicolas Cohanet was organist. According to at least one account, two fairly mediocre organs preceded the organ of 1636.

On January 22, 1631, five years after the church's dedication, a contract for a new organ and organ case was signed by the churchwardens of the parish. Jehan Buron, a master woodworker, was contracted to design and construct an organ case. Pierre Le Pescheur, an organ builder whose house adjoined the church, was hired to construct the organ itself.

Buron began work on the case immediately, because it had to be completed the following year. The case he built is often cited as the most beautiful in Paris. Norbert Dufourcq was more effusive, describing it as “one of the most perfect masterpieces of seventeenth-century European woodwork.”

Le Pescheur's organ of four manuals (forty-eight notes) and pedal (thirty-two notes), with thirty-four stops, was installed in 1636. Very little of this organ remains in the current instrument. A restoration and enlargement of the organ, necessitated by a fire that destroyed much of the instrument, was begun by Nicolas Somer in 1760, and remained unfinished upon his death. In 1777 François-Henri Clicquot rebuilt the reeds, added an hautbois to the positif, another hautbois to the récit in place of the trompette, and a bombarde 16' to the pedal. The instrument was one of the rare organs spared during the ensuing Revolution, but not without some damage. In 1807, care of the organ was entrusted to Pierre Dallery.