The abbey was temporarily suppressed by the Jacobins in 1799. According to historical tradition, on 20 June 1859 the monks gave shelter to some patriots who, raising against the papal authority at the incitement of the main exponents of the local Freemasonry, clashed with the regiment of Swiss soldiers of the Papal States (the 1859 Perugia uprising). Consequently, after the intervention of the Piedmontese army and the long-awaited Unification of Italy, the new government allowed the Benedictines to remain in the abbey, granting an extension to the Pepoli decree which sanctioned the state ownership of the ecclesiastical property, until the religious persons present at the events of 20 June 1859 were reduced to three. When, in 1890, the third last monk died, Law no. 4799 of 10 July 1887 was implemented, which established that the property of the suppressed abbey of San Pietro was to be used for the creation of an "Institute of Agricultural Education" to be founded in Perugia, currently the Department of Agricultural, Food and Environmental Sciences of the University of Perugia.
