In 1847, Pope Pius IX, with the Apostolic Letter Nulla celebrior, re-established the Latin Patriarchate in Jerusalem. The document recalled the obstacles that had hitherto prevented the Latin Patriarch from residing in Jerusalem and restored the exercise of jurisdiction of the Latin Patriarch in Jerusalem. During this time, the Franciscans in the Holy Land continue to fulfill their providential mission to care for the holy places and to expand activities for the people in this area to whom they were missioned.
A number of shrines were acquired over the course of the years: In 1867, Servant of God Pauline Nicolay gave the Custody the shrine at Emmaus; in 1875, the 7th Station on the Via Dolorosa was acquired; in 1878, the shrine of Naim; in 1879, talks concluded over the shrine at Cana; in 1880, the shrine of Bethpage was acquired; between 1889-1950, the Custody acquired the right to take possession of the 5th Station, the "Dominus Flevit", Tabgha, Capernaum, the Shepherds' Field near Bethlehem, the Monastery of St. John the Baptist in the Desert, Mount Nebo, the place of Jesus' baptism on the banks of the Jordan, a small place in the immediate vicinity of the Holy Cenacle and Bethany.
During this period the Custody of the Holy Land played a role in the partial or total reconstruction of the shrines. These often consisted of small, unpretentious chapels. For economic reasons and those of social resistance, it was not possible to do more.
The Franciscans endeavored to maintain the shrines in a spirit of dignity and devotion proper to the needs of the faithful. A record of construction projects include the following: the Basilica of Emmaus in 1901; the Basilica of the Agony at Gethsemane between 1919-1924; the Basilica of the Transfiguration on Mount Tabor between 1921-1924; the new shrine at Bethany between 1952-1953; the Chapel at the Shepherds’ Field near Bethlehem between 1953-1954; the Church of "Dominus Flevit” on the slopes of the Mount of Olives in 1955; and the Basilica of the Annunciation in Nazareth between 1955-1969.
During this period, more friars’ blood was spilled. In 1860, persecutions arose against Christians by the Druze in Lebanon and in Syria. The persecutions were sparked by a decree signed by Sultan Abdul-Mejid in Paris in 1856, in which he recognized the equality of all his subjects, without distinction of race or religion. The persecutions led to about 7,000 deaths, among them Blessed Emmanuel Ruiz and his martyred companions. Another case of martyrdom took place in Turkey in 1895, when Friar Salvatore Lilli was killed. He who was later canonized.
The historical climate of the early Twentieth Century can be better understood by reading the chronicles of that period. In 1901, bloody attacks arose partially due to tensions concerning the status quo. On one occasion, Greek monks stoned friars over whose right it was to sweep the square next to the stairs that led to the so-called chapel of the Franks. In 1920, Turks killed three priests and two friars over tensions related to the persecution of the Armenians.
In conclusion, Pope Paul VI, in his Apostolic Exhortation Nobis in animo (1974), gave an historical overview of the Custody of the Holy Land: "Not without a providential plan have the historical events of the thirteenth century been brought to the Order of the Friars Minor in the Holy Land. The children of St. Francis have, since then, remained in the Land of Jesus for several consecutive years to serve the local Church and to preserve, restore, protect the Christian Holy Places; their loyalty to the desire of their founder and to the mandate of the Holy See was often sealed by acts of extraordinary virtue and generosity.”