This period was marked by uncertainty for the papacy and the Roman Catholic Church following the invasion of the Papal States and abduction of Pius VI under the French Directory.

At the beginning of his pontificate he promised to continue the work of his predecessor, Clement XIV, in whose 1773 brief Dominus ac Redemptor the dissolution of the Society of Jesus was announced.

The Archduchy of Austria proved a threat when its ruler, Emperor Joseph II, made internal reforms which conflicted with some of the power of the Papacy.

At the outbreak of the French Revolution Pius was compelled to see the independent Gallican Church suppressed, the pontifical and ecclesiastical possessions in France confiscated, and an effigy of himself burnt by the populace at the Palais Royal.

The Treaty of Tolentino transferred Romagna to Bonaparte's newly formed Cispadane Republic (founded in December 1796 out of a merger of Reggio, Modena, Bologna and Ferrara) in a hope that the French would not further pursue the Papal lands.

Louis Alexandre Berthier marched to Rome, entered it unopposed on 13 February 1798, and, proclaiming a Roman Republic, demanded of the pope the renunciation of his temporal authority.

The French declaration of war against Grand Duke Ferdinand III of Tuscany led to Pius' removal, though by this time deathly ill, by way of Parma, Piacenza, Turin and Grenoble to the citadel of Valence, where he died six weeks later, on 29 August 1799.

The city, along with other northern Italian lands, was held by the Archduchy of Austria, whose ruler Francis II, Holy Roman Emperor, agreed to defray the costs of the conclave.

As the conclave was in the third month Cardinal Maury, who supported neither Bellisomi nor Mattei, suggested Gregorio Barnaba Chiaramonti, OSB Cassin., the Bishop of Imola.

Following this promotion[clarification needed], Bonaparte decided to recognise the new pope and restored the Papal States to those borders set out at Tolentino.

Fearing further invasion he decreed the Papal States should remain neutral between Napoleonic Italy in the north and the Kingdom of Naples in the south.

On 15 July France officially re-recognised Catholicism as its majority (not state) religion in the Concordat of 1801, and the Church was granted a measure of freedom with a Gallician constitution of the clergy.

The newly crowned emperor of the French restarted his expansionist policies and assumed control over Ancona, Naples (following the Battle of Austerlitz, installing his brother Joseph Bonaparte as its new king), Pontecorvo and Benevento.

The changes angered the pope, and following his refusal to accept them, Napoleon, in February 1808, demanded he subsidise France's military conflict with the United Kingdom of Great Britain and Ireland.