In around 1025, Oliba, Abbot of Ripoll, and Bishop of Vic, sent a group of monks to Montserrat to settle at the small Church of Santa Maria. The monks of Santa Cecilia had established themselves on the mountain 75 years ago, and their monastery was independent and had the title of abbey. After a short period of time, the monks of Santa Maria de Montserrat rebuilt the church; the monks from Santa Cecília also carried out restoration on their church, adding three apses with arcades and Lombard Romanesque fascias. Subsequently they reinforced the walls in order to cover the church with a barrel vault.
While the Monastery of Santa Maria de Montserrat grew fast and soon became famous for the huge influx of pilgrims attracted by the holy image, the Monastery of Santa Cecilia barely survived. By the fourteenth century, the decline of Santa Cecilia was evident and its main function was ministering to the parish exercise and providing accommodation for pilgrims on their way to Santa Maria.
The decline of Santa Cecilia de Montserrat reached its low point when the abbots in charge of the monastery were no longer monks from the site, but external ecclesiastics who held the title and received the income from the monastery.
In 1537, Pope Julius II, who had been abbot of Santa Maria de Montserrat, issued a decree that added the Monastery of Santa Cecilia to the Monastery of Montserrat in perpetuity. From that moment on, just one priest who served as the parish rector lived at Santa Cecilia.
In 1811, general Suchet ordered the destruction of Montserrat, which had become a symbol of resistance against the Napoleonic invasion. On that occasion, the Church of Santa Cecilia de Montserrat was also badly damaged.
In 1866, after the laws decreeing the confiscation of church property and the expulsion of communities had been repealed, Miquel Muntadas (1809-1885), Abbot of Montserrat, commissioned the architect Francesc de Paula Villar Lozano (1828-1903) to carry out the restoration of Santa Cecília. Villar repaired the serious damage that had been done to the deteriorated church building. The left-hand apse was rebuilt, the spurious door that had been opened in the central apse was closed, and the main door was returned to its original state. However, the exterior and the Santa Cecilia site generally continued to present the appearance of an abandoned building until restoration by Puig i Cadafalch in 1928-1931.