By the terms of this agreement the Este family relinquished their claim to the duchy of Ferrara, but Cesare's excommunication was lifted, the family properties were left to them while their moveable assets could be transferred to Modena. The artillery was divided equally between the two parties.
On 28 January 1598 the last of the Estes left Ferrara through the Porta degli Angeli with tears in his eyes and the next day Cardinal Pietro Aldobrandini entered the city to receive the keys from the magistrature. He immediately set about the task of ensuring public order, granted significant tax relief and ordered a generous number of amnesties.
A tribunal was set up to settle legal suits but the Cardinal reserved himself the power to elect the podestà without consulting the citizenry. But Clement VIII intended to take possession of the city personally and on 12 April he set out for Ferrara, where he arrived on 7 May.
The papal retinue was of a theatrical sumptuousness and symbolized the Vatican's particular blend of spiritual and temporal power: travelling one day ahead of the papal train came the Blessed Sacrament, contained in a crystal urn covered by a little canopy and borne by a white horse with a silver bell round its neck.
The Pontiff took pains to control the situation in the city and surrounding countryside by establishing the Costituzione Centumvirale, a Council of a hundred citizens representing the population.
He also renewed the licences of mills, inns and butcheries, tackled some urgent general problems such as those regarding the waters and rivers, and paid personal visits to the most important areas around Ferrara.
In the meantime, the papal presence in Ferrara was attracting ambassadors and special envoys of sovereigns, princes and city states. On 14 October 1598 the city was the scene of the funeral of Philip II of Spain while, on the following 15 November, it played host to the double wedding of Philip III of Spain with Margaret of Austria and Albert of Austria with Isabella, daughter of Philip II. The Pontiff, after blessing the people in the Cathedral, left Ferrara on 27 November by the Castel Tedaldo gate, which was definitively closed immediately after.
He attached so much importance to direct papal rule of the city that, once back in the Eternal City, he decreed that every year, in Rome, the day of Cardinal Aldobrandini's entry into Ferrara would be commemorated with a solemn Mass and various secular displays.
But papal control of the city could not evidently count on the loyalty of the people of Ferrara. The Pope himself ordered the cannons on the city walls to be pointed at the city: a severe warning to anyone thinking of rebellion.