Between 1863 and 1868, the organ was largely rebuilt by Aristide Cavaillé-Coll, incorporating some older pipe material. Over the following decades, several modifications were made: in 1904, Charles Mutin expanded the stoplist; in 1924, an electric blower was installed; and in 1932, Joseph Beuchet undertook renovations that included changes to the manuals, mixtures, and wind pressure distribution. Starting in 1959, Jean Hermann electrified the key and stop actions and installed a new console. Additional changes to the stoplist followed, implemented by Robert Boisseau and later by Jean-Loup Boisseau. Due to safety concerns, the setter system was decommissioned in 1983.

A major overhaul between 1990 and 1992 involved several prominent organ builders, preserving components from the Jean Hermann console while modernizing and expanding the instrument. From 2012 to 2014, Bertrand Cattiaux and Pascal Quoirin carried out further restoration, including a new swell division ("Résonnance expressive") and a general cleaning and tuning. Although the organ was damaged by smoke and debris during the 2019 Notre-Dame fire, it miraculously survived intact and dry. After securing the building, the instrument was carefully dismantled and distributed among three workshops for restoration. By late 2023, key components like windchests and bellows were refurbished, and reassembly began. The organ was first heard again during a Mass on December 7, 2024, marking its return to liturgical life.

Additionals: II/I, III/I, IV/I, V/I; III/II, IV/II, V/II; IV/III, V/III; V/IV; I/P, II/P, III/P, IV/P, V/P, sub- and superoctave couplers, Octave grave général, Inversion Positif/Grand-Orgue, 2 swell pedals (Récit and Résonnance expressive), Trémolo III, Tremblant Résonnance

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