The palace bore several names: Palazzo del Governatore di Borgo, Palazzo delle Prigioni di Borgo, Palazzo del Soldano or Palazzo dal Pozzo. The first two denominations were linked to its public functions (governor's residence and jail). The third derived either from having been the prison of Turks captured during the Battle of Lepanto, who were imprisoned here for a short time, or from having been the seat of the "Soldano", that is, the chief of the papal police. The fourth derived from its having been the residence of the dal Pozzo family.
Ferrari probably died during the Sack of Rome in 1527, and the ownership of the palace passed to Pietro Paolo Arditio, notary of the Apostolic Chamber. According to Gustavo Giovannoni, the palace was built instead by Guglielmo dal Pozzo, apostolic protonotary, who died in 1527 and was buried in Santa Maria in Traspontina. Giovannoni bases this attribution on his discovery of two coats of arms of the dal Pozzo family carved on two keystones in the hall and in the courtyard of the building. However, no document related to the building in which the name of dal Pozzo is mentioned has been found so far.
In 1571 an heir of Arditio, Girolamo, sold the building to the Apostolic Chamber. The Chamber destined it to the seat of the curia of the Governor of the Borgo (district at that time separated from Rome), the relative court and the prisons; the latter replaced the jail in the Giustina tower near Palazzo Cesi, after its demolition. The office of Governor of the Borgo was established by Pope Julius III (r. 1550–1555) on February 22, 1550, and abolished by Clement X (r. 1670–1676) in the year of his death. The jurisdiction of the magistrate extended from the S. Pietro gate by Castel Sant'Angelo to Porta Settimiana in Trastevere. Being a key position, the governor was almost always a relative of the pontiff.
During this period the building witnessed truculent events and hosted important persons in its prison, which was similar to other Roman jails but without necessary services such as the infirmary. In 1561 a boy working by the osteria del cavalletto ("easel inn") in Borgo Vecchio, accused of theft, after confessing jumped from a window of the building. Although he had died in the nearby Santo Spirito hospital, he was sentenced to be hanged dead in front of the inn where he had worked. In September 1596 Francesco Cenci, the depraved father of Beatrice, was a guest of the prisons of Borgo for a month; he was convicted after having been surprised in an act of love with the wife of a shoemaker. Cenci had been sentenced to be whipped but was able to avoid punishment thanks to the intercession of the Cardinal Anton Maria Salviati. In March 1599 three guards of the Bargello were hanged in front of the prisons after having been accused of burglary against the "procaccio of Naples", the postal courier for the campanian city, which they were supposed to escort.
In 1676 the palace was transformed into a rental house, and with the years it deteriorated greatly: at the time of its demolition in 1936 it was devoid of the window pediments and aediculas. The architects Marcello Piacentini and Attilio Spaccarelli, designers of via della Conciliazione, demolished the ancient building, whose reconstruction was originally planned, saving only the portal which, surmounted by an attic to bring it to the level of the portals of the other edifices of the road, was reassembled on the new building in via della Conciliazione n. 15.
According to Paolo Portoghesi, Palazzo dal Pozzo is one of the first works showing the artistic maturity of Sangallo, whose culture was "now free from uncertainties and consciously directed to the re-acquisition of classical elements".