He probably began his musical career as a singer in a choir of a local church. Later he studied to become a priest in the cathedral at Valencia, which included lessons in music. On 15 May 1665, at 20 years of age, he was named the assistant organist of the cathedral. A year later, upon the death of his predecessor, he became the principal organist. On 22 September 1668 he was ordained as a priest. He kept his position as principal organist for 45 years, but from 1703 on his health often necessitated that a substitute be found. From 1675 to 1677 he also took charge of teaching the children in the cathedral choir. No portrait or likeness of Cabanilles is known to exist; the portrait accompanying certain Facebook pages and other internet articles is of the botanist Antonio José Cavanilles (1745-1804).
Many of Cabanilles's compositions are virtuosic and advanced for their time, but generally, he is in the Spanish tradition of keyboard music following 16th century patterns. The majority of his manuscripts are kept in the Biblioteca de Catalunya in Barcelona. Numerous compositions for organ (tientos,toccatas,passacaglias, and other works) have survived, as well as a number of works for choirs of up to 13 parts.