Construction work on the church and adjacent convent of St Claire began in 1257
, three years after the saint's death and a year after she was canonised.
Until then the sisters of St Claire had lodged at San Damiano. The church dedicated to St Claire occupied the site of the church of San Giorgio
, where St Francis had been buried before his remains were moved to the basilica in 1230.
The exterior of the building makes use of alternate strips of pink and white stone
, with massive supporting arches either side.
The interior has the same layout as the Upper Basilica of St Francis, with a single nave that terminates in a transept and polygonal apse. Like St Francis', a gallery runs the entire perimeter of the church, although here it is on the same level as the capitols. On the right hand side of the nave the Cappella del Crocifisso and the Cappella del Sacramento were once part of the nave of the previously existing church of San Giorgio, where Pope Gregory IX canonised St Francis in 1228.
The wooden "Crucifix“ in the Cappella del Crocifisso is alleged to have spoken to St Francis in San Damiano, ordering him to repair the church. Relics of St Francis and St Claire are kept behind the grate. The following chapel contains a fresco by Puccio Capanna (1340-46): "Enthroned Madonna and Child with St Claire, St John the Baptist, the Archangel Michael and St Francis", as well as other frescoes of the school of Giotto and Lorenzetti
The right hand transept contains a panel with the "Life of St Claire“, by the so-called Maestro di Santa Chiara (late 13th century), as well as frescoes depicting St Claire and Biblical scenes by an artist known as the Maestro Espressionista di Santa Chiara (first half of the 14th century). The "Crucifix“ in the apse has also been attributed to the Maestro di Santa Chiara (1280-90).
A colonnade of 12 polygonal columns carved by a local workman in the 15th century encloses the high altar. The wrought iron dividing curtain is 17th century. A detached 14th century fresco of the "Nativity“ displays influences of Giotto in the left hand transept.
The Byzantine style Hodegetria type panel on the left hand wall depicts the "Madonna and Child“ and is by an unknown artist from the 13th century. The lunettes are decorated with scenes from the Old Testament similar to those in the upper cycle of the Upper Basilica of St Francis (late 13th century).
The crypt was built between 1850 and 1872. Restored in neo-gothic style in 1935, it houses the body of St Claire, disovered in 1850.