The French Revolution proved as disastrous for the temporal territories of the Papacy as it was for the Roman Church in general. In 1791 the Comtat Venaissin and Avignon were annexed by France. Later, with the French invasion of Italy in 1796, the Legations were seized and became part of the revolutionary Cisalpine Republic.

Two years later, the Papal States as a whole were invaded by French forces, who declared a Roman Republic.Pope Pius VI died in exile in Valence (France) in 1799. The Papal States were restored in June 1800 and Pope Pius VII returned, but the French again invaded in 1808, and this time the remainder of the States of the Church were annexed to France, forming the départements of Tibre and Trasimène.

With the fall of the Napoleonic system in 1814, the Papal States were restored once more. From 1814 until the death of Pope Gregory XVI in 1846, the popes followed a reactionary policy in the Papal States. For instance, the city of Rome maintained the last Jewish ghetto in Western Europe. There were hopes that this would change whenPope Pius IX was elected to succeed Gregory and began to introduce liberal reforms