After Matthias' death, he travelled frequently to Italy. During one of these trips, he was created cardinal by Alexander VI, on September 20, 1493. Three years later he returned to Italy to escape the plague that was striking Hungary and arrived in Rome with a following of 250 people. He was appointed archbishop of Milan in 1497 and named cardinal in 1509, after which he resided in Rome and governed the archdiocese of Milan through a vicar. According to the tax reports of the Curia for the year 1500, he was the fifth richest member. His influence grew further when his brother Alfonso married Lucrezia Borgia, daughter of Alexander VI, who granted him the title of archipresbyter of St. Peter's. He remained in Rome until February 15, 1503, although his relationship with the pope later deteriorated due to Ercole's philo-French maneuvers.
After Alexander's death, Pius III appointed him bishop of Ferrara, but Ippolito was again at odds with his successor Julius II, and in 1507 he left the Curia. However, the following year Julius praised him for his conduct in the Bentivoglio plot. In 1509 he successfully led a military contingent to regain the Polesine territories that the Este had lost in the war with Venice in 1484, winning the decisive battle of Polesella. On July 27 the pope recalled him to Rome, but, feeling his life was unsafe, Ippolito fled to Hungary.
On May 16, 1511, he was among the cardinals who signed the appeal to the pope to speak at the schismatic Council of Pisa. However, his brother Alfonso later convinced him to abandon the schism, and the pope authorized him to return to Ferrara. In 1513 Ippolito moved again to Hungary but, when in his absence Leo XMedici was elected pope, he returned again to his native city. On April 22, 1514, he and his family were pardoned for all their past anti-papal acts.
He died in Ferrara during his last return to Italy from an indigestion of lobsters. He was buried in Ferrara Cathedral. His estate, inherited by Alfonso I, amounted to some 200,000 ducati. Ippolito had two illegitimate children.