After Pope Innocent's election, though, d'Este had a falling out with members of the Spanish faction of the College of Cardinals who had been the driving force behind the Pope's election against candidates put forward by the French faction. After the falling out, d'Este declared himself for France. As a result, though his family had previously been in conflict with the Barberini, he became their ardent supporters while they were in exile in France.[2] He returned to Modena and became temporary ruler when his brother left to fight the Spanish in 1647.
Later he returned to Rome upon hearing that the Admiral of Castile was visiting as ambassador of the Kingdom of Spain. The Admiral, though, saw every cardinal except for d'Este on the grounds that d'Este had declared himself for France.[2] The slight escalated and both the Admiral and Cardinal d'Este raised 600 men-at-arms each in preparation for armed conflict; d'Este having pawned jewels to hire militia as neither his family nor his French supporters had been able to raise funds quickly enough. Eventually, the conflict was quelled when Pope Innocent ordered his own troops to enter Rome to keep the peace, though several militiamen on both sides were killed.[2]