The church has only one nave that is particularly lengthened and cut cross-wise by seven ogival arches and ending in a polygonal apse including a large Gothic mullioned window.
The covering of the nave is made of wooden beams resting on huge arches, whereas the apse is covered by a vault with ribs featuring polygonal sections, supported by small embossed columns with foliar capitals.
The walls are decorated with a series of frescoed scenes, partly patchy: particularly interesting on the left are a Majesty, some Saints and a popular-style Crucifixion with St. Francis and the donor at Christ’s feet made by an unknown Umbrian artist of the 14th century; on the inside of the façade there is an Adoration of the Magi attributed to Livio Agresti. The elegant Renaissance bust of St. Bernardino made of polychrome terracotta is attributable to the school of Vecchietta.
Behind the building there is an elegant cloister where art and craft exhibitions take place every year. Both the official document and the precise date of the Friars Minor settlement in San Gemini are unknown: the tradition follows what the biographer of the St. Tommaso da Celano wrote about the arrival of St. Francis in town. The church was however built before 1291, year when Nicholas V, with a papal Bull, granted particular indulgences to some Franciscan buildings including this one in San Gemini.