In the place where today stands the church there was a pagan sanctuary with a source that in the Etruscan-Roman period was consecrated to Apollo, while in the early Middle Ages it was called Fonte Tecta.

The construction of the church took place between 1435 and 1444 : on a design by Domenico del Fattore, a late Gothic building was erected, with a single nave, cross vaults and a shallow apse. Dating between 1477 and 1481 is the fresco with Pope Sixtus IV enthroned with Cardinal Gonzaga and the cardinal Piccolomini in the act of granting the indulgence requested by the priors for the patrons of the sanctuary, of Lorentino d’Andrea. On the right side, after the death of Saint Bernardino (1444) the chapel dedicated to him was added.

Custodians of the church of Santa Maria delle Grazie are the friars of the order of the Discalced Carmelites who took possession of it in 1695 and have maintained, without interruptions, their ownership until today. On 13 June 1786 the Grand Duke of Tuscany, Pietro Leopoldo I decided to suppress the convent of Santa Maria and the friars were forced to leave on 24 August of that same year. A chaplain from the Arezzo church of Santa Croce took over and remained there for about two years; subsequently it was the same parish priest of Santa Croce who settled there and sold the part of the convent not used to Donato Redi of Arezzo; also the portico that surrounded the lawn in front of the church was sold to the municipality of Arezzo which will provide for its almost total demolition in 1788.

Said portico will only be partially brought to light and rebuilt in the 70s of the 900. Following the death of Pietro Leopoldo and the interest of the population of Arezzo the Carmelites returned to the possession of a church and a convent on the 21st January 1793 and the previously sold goods were bought back. In 1810 the Carmelites forcibly left the convent following a Napoleonic decree and remained outside for more than five years. After the unification of Italy the friars had to undergo several attempts to expropriation, but managed to maintain the ownership of the church.