The exact date when Amelia became a municipality is not known, but it is historically established that the city fought a war between the common side of Todi and Foligno against Perugia, Orvieto and Gubbio in 1065: it seems, therefore, that at the time it had a significant municipal organization. Charged with the regency of the City were Consuls (two or four), who were elected among the most representative men of the city.

In 1208, the Abbey of San Secondo entered into a peace treaty-submission with Todi, which aimed to keep it tied with Amelia, whose control was vital to remove the interference of Orvieto, a bitter enemy. As part of the struggle between the Papacy and the Empire, the city of Amelia underwent a sack by the troops of Frederick II in 1240.

The decline of the City followed its involvement in the disputes between the Guelphs and Ghibellines. In the end of 1200, the city was governed by Popular Statutes which are preserved in the Historical Municipal texts of 1330 and 1346. Around the middle of the fourteenth century, Amelia was re-conquered by Cardinal Egidio Albornoz, who managed to remove several heavy burdens that the city had contracted against Todi. He also applied some changes to the Riformanze, preserved in the Historical City, with other codes and statutes, examples of legislative art that show how functional the municipal law was.

Between the late fourteenth and early fifteenth century, Amelia ran into a period of famine, whose effects were further aggravated by taxes imposed by Rome. The 11th November 1417, Cardinal Otto Colonna (Martin V) was elected Pope, and, having frequented Amelia, confirmed the privileges of the city. In 1426, St. Bernardino of Siena preached in Amelia against blasphemy and usury. However its belonging to the Church and the deriving influence, Amelia continued to strongly defend  the criteria of autonomy and municipal freedom, also encouraged by the auspices of distinguished Amerini, as Msgr. Angelo Geraldini.

In 1476, Pope Sixtus IV, moving away from Rome where the plague was raging, was hosted by the Geraldini in Amelia.