Francis of Assisi in his lifetime became an extremely popular preacher, particularly in Umbria, and in practically every town there were groups of his followers.
It was common at the time for monastic complexes to be located outside of the city boundaries, in order to maintain greater independence from the local bishops.
The Capitoni family was the main patron during construction of the church, their coat of arms is shown prominently in the capitals of the entrance door jambs.
In this period probably all the 14th century fresco decorations are painted over and the church takes a more sober Renaissance interior décor.
At this time, it seems that the apse's decorations are redone with new wall and vault paintings, in the front of the church over the entrance a wood choir is built, and the rose window is replaced with a rectangular one.
The altar is redone, and a low wall separates the presbytery from the apse, and the bell tower is repaired or rebuilt.
The approach taken at the time was to bring back the church to its original medieval state mostly by the removal of the additions and decorations introduced in the 18th century.
Since little remained of the medieval decoration, the result of this approach is that the interior walls are blank with a few fragments of mural paintings.
In 2020, the San Gemini Preservation Studies Program and the Associazione Valorizzazione del Patrimonio Storico Onlus will start a campaign to restore the front façade of the church, involving the cleaning and pointing of the stone masonry.
This simple white limestone façade is a good example of plain the Franciscan-Gothic architecture, it expresses their religious ideology of poverty and simplicity.
The decorated door jambs, like the apse, show a richer quality of gothic details that probably came at the end of the construction.
On the capitals of the engaged columns one finds the coat of arms of the Capitoni family, indicating their patronage of the church.
Above the portal there is an arched niche with a mural depicting Saint Francis painted in the 1950s by the local painter Tullio Bertozzi.
The roof is supported by a series of transversal pointed arches in brick construction that rest on stone brackets on the side walls.
Churches in this period were built slowly over many decades and often show variations in the architectural styles that take place during their construction.
On the left side there is a 17th-century wood pulpit with caryatids installed on top a more recent confessional; it is accessed from the sacristy.
The columns, capitals and ribs of the apse are in a more elaborate style stonework similar to what is found on the front portal of the church.
The rear Gothic style window with stained glass depicting St. Francis St. Gemine, St. Rocco and St. Matilda is new and was all done in the 1950s.