The church of San Michele in Cipriano was built in 720 in the "borghicciolo", an extension of the suburb of San Gervasio.
The current church was rebuilt in 1195 because of its poor condition and a collapse that happened in the twelfth century, probably reusing ornaments and pillars of the older church.
In 1260 it was called "Ecclesia S. Michaelis de Borghiciolo". In 1433, the Prior of San Bartolomeo in Silice gave the nun Marchesana di Pagano Portici, Mother Superior of the Sisters of the Third Order, the Church of St. Michele, an adjacent house, a vegetable garden and other property belonging to the Church.
In 1460 the church was consecrated and the Monastery saw the number of nuns who submitted to the rule of St. Chiara grow.
From the early 1500s to the late 1700s various works were carried out for the restoration and decoration that affected both of the Church and of the Monastery. In 1806, according to the decree of the Baciocchi Government, which provided for the removal and forfeiture of property of religious communities within the Principality of Lucca, the Monastery of San Micheletto was used as stables for the residence of the Villa Buonvisi.
In 1827, with the nuns coming back, there was a transition from private ownership to the community of nuns, who demanded the closure of the alley between the monastery of San Micheletto and of the monastery Della Visitazione with the construction of the wall separating them from the public square and allowing the exclusive use of the property common to the two monasteries.
In 1857, the restoration of the Church began. With the unification of Italy, the threat of the suppression of religious orders arose. In fact, in 1896 the City Council asked for and obtained the closing of the Monastery, but still allowing the nuns to use part of it.
In 1901, the City of Lucca returned the building to the religious order; later, fearing new oppressions, the religious community transferred ownership of the Monastery to the Opera Pia di Terrasanta. In 1945, the Monastery, inhabited by a small number of nuns, began a series of rent agreements with schools, regarding the majority of the north wing of the complex.
With the abandonment of the building by the nuns, in 1972 San Micheletto became property of the Cassa di Risparmio di Lucca.