Cabanilles was born in Algemesi, and his first name is shown variously as Juan and Joan; some works ascribed to "José Cabanillas" are now confirmed as belonging to his output and not that of another composer. Outside of his baptismal certificate, nothing is known of him until 1665, when the 21-year-old Cabanilles was appointed second organist at Valencia Cathedral, replacing the departing Jerónimo de la Torre. Somehow the issue that Cabanilles was not yet a priest was discreetly avoided, and thus he was not prevented from being promoted to first organist in April 1666. Cabanilles was finally ordained as a priest in September 1668. From then on, little is known of Cabanilles' activity, although he is said to have traveled north to France on occasion to play certain high holy feast days. In 1703, his health began to decline, and Cabanilles soon began to rotate a number of substitute organists in order to keep his position filled in Valencia. He died there, aged 67, in 1712.
Much of what is known, and the survival of many of Cabanilles works, is owed to the industriousness of his student Josep Elias. The manuscripts that Elias conserved and others of Cabanilles reside within the Library of Cataluña in Barcelona, which also publishes an edition of the works of this composer. Cabanilles' surviving output is rather extensive, numbering to nearly 200 pieces, all but eight written for the organ. Ninety are Tientos, monothematic in nature and based on the Renaissance form of the ricercar. Cabanilles' Tientos de falsas are noted for their liberal use of chromaticism and dark modal coloring. This approach has led some writers to cite Cabanilles as a harmonic revolutionary, but his approach is likely more reactionary. Cabanilles was one of the lone holdouts to Renaissance mannerism in an era where greater Europe was concerned with Baroque forms and major/minor key orientation. Nonetheless, Cabanilles' style was in keeping with trends in seventeenth century Spain. Cabanilles also composed polyphonic elaboration of chant and several works in variation form over a repeating bass figure, which he variably called passacalles, galiarda, paseos, and xacara. Cabanilles also experimented in six works with the Italian form of toccata. Of his Battle Pieces the famous Battala Imperiale has been discovered to be the work of Johann Kasper Kerll, not Cabanilles.
Valencia is a major port of call in Spain, and Cabanilles' music betrays some superficial elements derived from Italian practices, demonstrating that he knew contemporary Italian music. As the Kerll piece is found among Cabanilles' manuscripts, this seems to confirm his awareness of German music, and he may have known something about Franco-Flemish music as well. But overall, Cabanilles' music is overwhelmingly Spanish in character, and in his own time he was considered the last major figure in the line of "mystic" Spanish organists that begins with Antonio de Cabezón and continues through de Heredia, de Arauxo, and Coelho. Eight sacred vocal works survive in Cabanilles' catalog; a fragmentary mass, Magnificat, and six motets, of which the four-voice "Mortales que amais a un Dios immortal" utilizes a tune which would later coincidentally turn up in the St. Matthew Passion of Johann Sebastian Bach. His pupil, Josep Elias, who wrote, "the world will vanish before a second Cabanilles comes," gives an indication of the high regard in which Cabanilles was held in his day.