The monastery complex consists of the church of St Francis, naves of the female church and the Minorites monastery, the square cloister, the chapel of St Mary Magdalene, the church of St Salvator, the chapel of St Barbara, the monastery kitchen, the house abbess of the Order of St Clare and the enclosure walls.
Over the centuries the Monastery of St Agnes has undergone many changes and interventions, including Renaissance and Baroque style alternations. However, these were removed in the reconstruction in the 20th century. The monastery is a national monument and is now home to one of the parts of the National Gallery in Prague.
The Monastery is the oldest Gothic building in Prague and throughout the Czech Republic. The building of the convent of Poor Clares is the oldest preserved brick architecture in Prague.