The Revolution had a cruel effect on the music of the cathedral, which became a theophilanthropic temple dedicated to Reason. The break up of the Chapter in 1790 soon brought the same fate for the choir school. At twelve until then, the number of students began to plummet dangerously. The four tenured organists, Balbastre, Beauvarlet-Charpentier, Nicolas Séjan and Claude-Etienne Luce, were dismissed in 1793, the year the Conservatoire de Paris was founded. In 1802, under the Consulate, Pierre Desvignes (1764-1827) was appointed chapel master. The musician from Burgundy, student of Lesueur and Conservatoire teacher, enjoyed a certain renown. M. Cornu, former sub-master, then attempted to breathe new life into the moribund establishment. However, there were insufficient funds to provide the children with a suitable education. The saving grace came in 1807: a ministerial decree from the ministry of Public Instruction officially recognised the existence of the choir school, to which the emperor granted an annual subsidy of 3000 francs. All that remained was to assign the establishment a more secular status: musical teaching would have a major role to play so that the students could continue to fulfil their role in the liturgical life of the cathedral; but they would also benefit from a general education which would allow them to take up the career of their choice afterwards.
With the fall of the empire, fresh difficulties emerged: subsidies collapsed, the number of students dwindled again, and it needed the energy of one Joseph Pollet (in turn choir school member, music teacher, tenured organist, then chapel master over forty-one years, from 1831 to 1872) to restore the musical status of the cathedral. Msgr. Jehan Revert recounted humorously how, over the years, the liturgy was adapted to the political circumstances: "Without doubt, for everyone, the last verse of the 19th Psalm rewords the prayer “Domine salvum fac” and the musical scores still bear the mark of words barred out or overwritten: “imperatorem”, “regem”, and then “imperatorem” again and finally “salvam fac rempublicam”, and all of this with the drone-like royal tone, which as legend has it, was composed by Louis XIII…"
In 1872, Joseph Pollet resigned. Auguste Kiesgen replaced him for three years (1873-1876), before being succeeded by Charles Vervoitte (1819-1884), who had been Saint-Roch chapel master until then. Inspector of religious Music at the ministry of Public Instruction and Cults from 1771 to 1880, president of the Academic society for sacred music, author of the gargantuan Archives des cathédrales (Cathedral archives), Vervoitte was an influential character. He held the position until his death and the abbot Charles Geispitz succeeded him until 1905.
During this period, ceremonies regained a certain prosperity. The cathedral was even the venue for an event of some importance: the conversion of the young Paul Claudel, a confirmed atheist, to the Catholic faith. The poet himself wrote of the episode, which took place on Christmas Day 1886. During the vespers, when the choir school was performing the Magnificat, the young eighteen-year-old man was overcome by the beauty of the Marian canticle. "In an instant, my heart was moved and I believed. I believed so strongly, with such an uprising of my being, with such powerful conviction and with such certainty that no ounce of doubt remained. From then on, all the books, arguments, all the hazards of a turbulent life, could not shake my faith or even affect it in any way. " A paving stone not far from the statue of the Virgin Mary immortalises this moment.
Unlike many instruments in the capital, the organ escaped miraculously unharmed from the troubles of the Revolution. Balbastre, who was able to keep a low profile and adapt his repertoire to the tastes of the time, was able to protect it from revolutionary vandalism. But the instrument suffered nonetheless and was silent for some years. It rediscovered its former grandeur thanks to the most renowned organ builder of his time, Aristide Cavaillé-Coll, who rebuilt it while Viollet-le-Duc took to restoring the building itself. The unveiling of the superb instrument, on March 6, 1868 brought together the greatest organists of the day – César Franck, Camille Saint-Saëns, Charles-Marie Widor, Alexandre Guilmant – alongside the tenured organist, Eugène Sergent. Nonetheless, it was only with the appointment of Louis Vierne in 1900 that the instrument truly found a tenured organist worthy of its greatness.