With the capture of Jerusalem by the Crusaders (1099), the Principality of Galilee was entrusted to Tancred of Hauteville, who established the capital in Tiberias. The Principality always remained a vassal of the Kingdom of Jerusalem, entrusted to families originating from the north of France, and specifically, from 1120, to the Bures dynasty from the Île-de-France.
A Latin bishop named Bernardo was already active in Nazareth in 1109-1110, head of a community of regular canons who carried out liturgical service and the welcoming of pilgrims. Under Bishop William (1125-1129), Bernardo’s successor, Nazareth became metropolitan archdiocese with jurisdiction over all Galilee and with two suffragan seats led by the abbot of Mount Tabor and the bishop of Tiberias.
The Grotto of the Annunciation was incorporated into a new solemn construction and was restored to being a destination site for numerous pilgrimages. The first testimony, written about the Crusader basilica, dates back to 1106-1107 and is by the Russian pilgrim Daniel, who tells of having seen a large and magnificent church erected in the centre of the village, which kept the grotto in which the angel declared the annunciation to Mary.
According to the testimony, the work for the construction of this impressive basilica began very early, probably thanks to the rich donations that Tancred made at the church of Nazareth. The basilica, served by regular canons , was next to the bishop palace and contained a guest area for welcoming pilgrims as well as a well-stocked library. Moreover, the archbishop had six knights and around one hundred and fifty sergeants at his command. The archdiocese became so rich that it could boast properties from the Levantine to southern Italy, a country that in 1172 had sixteen churches controlled by Nazareth.
The cathedral of Nazareth, in all its splendour, as proven by the archaeological remains, would most definitely have reflected the wealth and prestige of the archbishop. Besides the Annunciation, the Crusaders built at least two other churches, that of Saint Joseph and also of Saint Gabriel that included the well in which according to the Infancy Gospel of James, Mary met the Angel before receiving the annunciation in the dwelling.
Although there is no record of the amount of damage that the town suffered in the catastrophic earthquake that hit Syria and the city of Tyre hard on 29th June 1170, it is certain that Nazareth was subjected to the Muslim looting that followed the earthquake. The Nazarenes and religious people were captured and incarcerated. In December of the same year, spurred on by an appeal of Letard, Archbishop of Nazareth, Pope Alexander III wrote to the French Christians to ask for help for the town. Father Bagatti, who directed the excavations of Nazareth, believed that the church was also damaged in the earthquake. According to the archaeologist, the seism acts as a gap between the period of construction and that of decoration of the building, made possible by the contribution of France. The link between Nazareth and France must have been very close given that the architectural and sculptural style with which the cathedral was lavishly decorated is that of 12th century France, particularly of Bourgogne, Ile-de-France, the Viennois and Provence.
The Greek pilgrim Giovanni Focas of 1177 (or perhaps 1185) describes a grotto of the Annunciation that is different with respect to that of the first century and splendidly decorated. The indications let us believe that the construction and part of the decoration of the cathedral was already finished by the end of the century and before the Saracen invasions. In 1183, the inhabitants of Nazareth were besieged for the first time by the Saladin troops which were camped out on the surrounding hills, forcing the entire village to seek refuge within the strong walls of the church.
The church served as a fortress and protection even following the defeat of the "Horns of Hattin" in July 1187 when the inhabitants were besieged by the Emir of Saladin, Muzafar al-Din Kukburi. The siege led to the conquest of Nazareth, the killing of the inhabitants and the profanation of the holy building that, however, remained undamaged.
For around forty years, the city and its archdiocese remained in Muslim hands and only a series of truces and grants allowed the religious people to begin celebrating in the basilica again and welcome the pilgrims.
Nazareth and the road that connected to Acre officially returned under Christian control in January 1229 as a result of the agreement between Frederick II and the Sultan al-Malik al Kamil; the French control of the town was confirmed again in 1241, but it seems that the archbishop did not return there before 1250.
The last rich donation of sacerdotal furniture, paraments and vestments to the cathedral was given by Louis IX, King of France, who undertook a pilgrimage to Nazareth in March 1251.
Finally, in April 1263, the town was besieged by one of the Emirs of the Sultan Baibars: the village was plundered and the impressive Crusader basilica was destroyed forever. Spared from destruction, until 1730 the Grotto of the Annunciation remained the only place in the area still accessible to the pilgrims, who however had to pay a fee to the Muslim guards.