The church stands on the site of King Ine of Wessex's Schola Saxorum, or "Saxon School", a charitable institution for Saxon pilgrims. It was rebuilt in the 12th century.
Subsequently it was restored several times. In 1475 Pope Sixtus IV commissioned joining the church to the nearby Hospital of the Holy Spirit for foundlings (which Pope Innocent III had built and whose history is given in wall-paintings in the church's sacristy) and given a bell tower. In 1538–1545, Antonio da Sangallo the Younger, or Baldassare Peruzzi, rebuilt the church after it had been damaged during the Sack of Rome. An organ, which survives, was added in 1547. In 1585–1590, Pope Sixtus V had the exterior restored, giving the church its present façade by Ottavio Mascherino, inspired by a design of Sangallo). This facade has two stories, with Corinthian pillars dividing the lower one into five sections, and the upper divided into three sections. In the upper middle section is a circular window, and above that is the coat-of-arms of Pope Sixtus V. The façade is crowned by a pediment. It is strongly reminiscent of Renaissance architecture.
In the station for the first Sunday after the octave of the Epiphany instituted by Pope Innocent III, a procession carried the veil of Saint Veronica from Saint Peter's Basilica, with the Pope celebrating Mass in this church. Indulgences were granted to those that took part, and money was given to the poor.
The coat of arms of the church of Santo Spirito in Sassia
The church has a single nave, and 10 apsidal chapels along the sides. The counter-facade has a Visitation (1545) by Marco Pino, and a Conversion of St. Paul begun by Francesco Salviati and completed by Francesco Rubiale. The first chapel to the right in the apse, has a fresco of the Pentecost by the Florentine Jacopo Zucchi and his brother. The second chapel has an Assumption by Livio Agresti, who also painted the Trinity in the 4th chapel as well as frescoes in the third chapel. The 5th chapel has an Annunciation and an Ascent (1570) by Giuseppe Valeriano. The sacristy is decorated by stories of the Schola Saxonum by Guidobaldo Abbatini. The apse is frescoed (1583) by both Jacopo and Francesco Zucchi. The fifth chapel on the left has a Martyrdom of St. John the Evangelist by Marcello Venusti. The second and first chapels contain paintings by Cesare Nebbia, including a Coronation of the Virgin.