The basilica of San Giovanni in Conca dates from the 4th century, and was located in a residential quarter of the ancient city.

Bernabò Visconti had it connected to his new grandiose palace through a super-elevated walk, and was buried here in a monument by Bonino da Campione which is now in the Sforzesco Castle together with that of his consort, Regina della Scala.

In 1531, Duke Francesco II Sforza donated it to the Carmelites, who erected a campanile which was utilized as astronomical observatory in the 19th century.

In 1879, the church was shortened to allow the construction of the current Via Mazzini; in the occasion, the Gothic façade was attached to the apse.

Over the crypt are remains of the apse walls, with a single window and blind arches typical of the Milanese Romanesque.