Chiaravalle Abbey was founded between 1134 and 1135 in an uncultivated and marshy area to the southeast of Milano beyond Porta Romana, a region populated by numerous villages that were then encompassed into the property of the monastery. There was active support from the Milanese population, with regards to both the donation of land for constructing the complex and raising the necessary funds, bolstering the connection between the Cistercians and Lombardy's main city.
Nothing remains of the first settlement, probably consisting of provisional structures. The construction of the current church started around 1150-1160. The work began with the choir and the apse, in order to allow religious practices to begin as quickly as possible. In 1196, the first alters were completed, and on 2 May 1221, the archbishop of Milano, Enrico Settala, consecrated the finished church.
The work then continued with the building of the first cloister, located to the south of the church. During the 13th century, there were significant transformations in Gothic style; the originally planned barrel vaults were replaced by cross vaults, the transept was raised, and the originally square pillars were replace by circular structures in brickwork. The bell tower was added in 1347-1349, perhaps designed by Francesco Pecorari, who is credited with the building of the bell tower of the Milanese church San Gottardo in Corte which shows similar characteristics.