From the XI century a decisive renovation started. The monastic complex was organised around the early cloister, the cornerstone of each Benedictine monastery (5), and the church of the monastery was enlarged in two stages, the latter in mid-XII century when the building took the shape of a three nave basilica. These centuries are important for the Cairate convent, depending from Pavia diocese and obeying Emperor Frederick I. In 1176 the imperial army is encamped near the village and, most likely, Barbarossa himself spent the night before the battle of Legnano against the Lega Lombarda in the monastery guest quarters. Only a few sculptures of this epoch remain, some are in various museums of Milan and Gallarate, others are exhibited (6) in the room which in former times was used as the monastery kitchen.
In the XIV century the church was further modified: the apse of the central nave became quadrangular and a pointed arch was set on it. In the following century the church was decorated with frescoes: a fresco depicting a Saint Bishop (7) in the opening of the old bell tower and the frescoes of the left aisle apse (8). In mid-XVI century, following the post-tridentine instructions (Council of Trent 1545-1563), the church was divided in two parts: an outer part for the community separated by a partition wall against which the outer altar is placed, the inner part for the exclusive use of the cloistered nuns. The apse of the central nave was panelled and frescoed with the Assumption of the Virgin by Aurelio Luini in 1560 (9). The nuns’ burial crypt in stone seats is of the same period: it is under the centre of the nave of the inner church (10). These works were commissioned by abbess Antonia Castiglioni who, at the end of ‘500, had her room decorated with a frieze running under the ceiling where angels, exotic animals and arms are interposed with musical instruments of the time, this is the reason why the room is called the music chamber (11).