Duchess consort of Mantua
In 1615, Cardinal Vincenzo Gonzaga —younger brother of Ferdinando I, Duke of Mantua and Monferrat— settled in the castle of Gazzuolo near San Martino. Despite the education and upbringing received from the Jesuits, the 21-year-old prince exhibited very dissolute behavior, for which he was removed from the Ducal court. When he learned that a middle-aged cousin once considered to be one of the first Italian beauties lived close to him, he decided to pay her a visit: it turned out that the 39-years-old Isabella, mother of eight children, was still beautiful and seductive. Vincenzo fell in love with her, but she refused his advances; then he proposed to her. In August 1616, they secretly married in the chapel of the San Martino palace. Vincenzo asked Pope Paul V for his release from his ecclesiastical vows. On 5 September of that year, his renouncement of the cardinalate received an official approval.
Ferdinando I was against this wedding, as he expected to influence through his younger brother's ecclesiastical status the policy of the Holy See in favor of the House of Gonzaga. The Duke turned to the Bishop of Mantua with a request to declare the marriage invalid, in order to return Vincenzo to the cardinalate; his position was shared by his wife Catherine de' Medici, who even tried to convince her mother Christina of Lorraine to obtain the support of the Grand Duchy of Tuscany in this matter. At first Vincenzo desperately resisted, but when he was banished to Goito and deprived of a number of material advantages, he broke down, and in December 1616 agreed with his older brother's demands to have his marriage to Isabella annulled.
Isabella was kept under surveillance for some time in Gazzuolo, but when it was confirmed that she wasn't pregnant, she was allowed to return to San Martino. However, the annulment of her marriage with Vincenzo turned out to be very difficult. Ferdinando I, using the help of his wife's cousin, Queen Marie of France, received the conclusion of the Sorbonne professors about the possible annulment of the marriage because of the close relationship of the couple; however, this wasn't enough. In Mantua itself, members of the Sabionetta and Novellara branches of the House of Gonzaga spoke out against the divorce.
Ferdinando I, childless in his marriage, understood that his younger brother was his heir, and wanted Vincenzo to marry soon to secure the survival of the dynasty; so, after an unsuccessful attempt to poison Isabella, the Duke accused her of witchcraft. The accusations provoked the beginning of the inquisition process, which was opened in the diocese of Mantua in 1622. There were supposed "witnesses" who said that they saw the Dowager Lady of San Martino all’Argine using magical potions. Isabella soon understood that if she went through a witch trial in Mantua, she would likely have no chance to save her life, especially when the accusation of witchcraft was supported by her husband. In 1623, she fled to Rome and appealed her case to the Supreme Inquisition. Thus, a new process was initiated, which was approved by the new Pope Urban VIII. Ferdinando I vainly insisted on conducting the inquisition process in Mantua. Isabella, at the insistence of the Duke, was imprisoned in the Castel Sant'Angelo in Rome. But soon, after a thorough investigation, she was cleared of all charges of witchcraft. All the "witnesses" were summoned to Rome, and once there, they recanted their testimonies. During January and May 1624, she was fully rehabilitated. The next attempt of the Duke and her husband to kill her, using hired killers, also failed.
In October 1626, Vincenzo became the new Duke of Mantua and Montferrat, under the name of Vincenzo II. Although the couple lived separately, they were still legally married, so Isabella was given the title of Duchess consort of Mantua and Montferrat. This news reached her in Rome. In April 1627, the Holy See confirmed the validity of the marriage of Isabella and Vincenzo II. In addition, she raised the issue of material compensation for damages caused by her husband and his relatives, as well as her recognition as Duchess. In December 1627, Isabella was widowed for the second time. With the death of her childless husband, the main line of the House of Gonzaga became extinct, and the War of the Mantuan Succession began.