The Independence War marked the beginning of the 19th century, very conflictive for our Church, which suffered persecution and the extinction of religious orders, which re-emerged greatly diminished, as well as the consequences of the confiscation laws (1834 and 1837) that led to the total disappearance of the male monastic orders.

Great monasteries such as the Carthusian monastery of Vall de Crist (Altura, Castellón), the Cistercian abbey of Santa María de la Valldigna (Simat de la Valldigna, Valencia) and the Hieronymites monastery of San Miguel de los Reyes (Valencia) suffered a ruin from which only the last one mentioned, have recently been recovered, converted into the Valencian Community Library.

In the middle of the century, the recovery of religious life began with the construction of the new Metropolitan Seminary of the Immaculate Conception of Valencia by Cardinal Mr. Antolín Monescillo y Viso (1890), later erected into the Pontifical University by Pope Leo XIII (1897), under the direction of Canon Mr. Niceto Alonso Peruj author of the great Dictionary of Ecclesiastical Sciences (1883-1890), which he directed together with Juan Pérez Angulo and of one of the best editions of the Summa Theologica of Saint Thomas Aquinas. In both works he had another collaborator who would become Archbishop of Seville Mr. Salvador Castellote Pinazo.

New religious orders of a social and educational nature were also founded in Valencia such as The Adorers of Saint María Micaela of the Blessed Sacrament (+1865), The Little Sisters of the Helpless Elders, work of Saint Theresa of Jesus Jornet (+1897), the Servants of Immaculate Mary, founded by the Blessed Juana María Condesa Lluch (+1916) and other institutes of consecrated life such as the Cooperators of Betania, Sisters of Christian Doctrine, Franciscan Sisters of the Immaculate, Catechist Operators, Workers of the Divine Master (Hail Mary devouts), Trinitarians, Amigonians and Tertiary Sisters; as well as the foundation of Secular Institutes like the Workers of the Cross, Lumen Christi and Social Apostolate Members.

Emblem of the new religious and social vigor of the parishes was the secular virgin of Algemesí Josefa Naval Girbés (+ 1893), beatified in 1988.

The constant activity of the Valencian missionaries offered the Church two new martyrs, Blessed Francisco Bolta and Francisco Pinazo, Franciscans (+ Damasco, 1864).