In the middle of the 6th century it was captured by Totila after a long siege. In the Lombard period it is spoken of as one of the principal cities of Tuscia. In the 9th century, with the consent of Charles the Great and Louis the Pious, it passed under the popes; but for many centuries the city continued to maintain an independent life, warring against many of the neighbouring lands and cities--Foligno, Assisi, Spoleto, Todi, Montepulciano, and remaining loyal for the most part to the Guelphs (the Pope's party). On various occasions the popes found asylum within its walls, and it was the meeting-place of the conclaves which elected Honorius II (1124), Honorius IV (1285), Celestine V (1294), and Clement V (1305).
In the 15th century power was concentrated in the Baglioni family, who defied all other authority. Gian Paolo Baglioni was lured to Rome in 1520 and beheaded by Leo X; and in 1534 Rodolfo, who had slain a papal legate, was defeated by Pier Luigi Farnese, and the city, captured and plundered by his soldiers, was deprived of its privileges. A citadel known as the Rocca Paolina, after the name of Pope Paul III, was begun six years later "ad coercendam Perusinorum audaciam." In 1797, the city was conquered by French troops and it was finally united, along with the rest of Umbria, to the Kingdom of Italy in 1860.