Although Tromboncino was "much favored" by the Mantuan court, he began showing signs of a difficult disposition. As musicologist William Prizer puts it, "his career in Mantua seems to have been a stormy one." That may be an understatement.

Tromboncino fled to Venice in 1495 over an offense that was apparently egregious enough that he would return to Mantua upon his father's insistence. But it was in 1499 that he committed the act that has made him infamous in music history. In July of that year, Tromboncino discovered his wife in flagrante delicto–that is, in the act of adultery–and murdered her.

The blow-by-blow circumstances of the murder are related in a letter from the patron Isabella d'Este to her husband requesting that he pardon Tromboncino: “Today around five o’clock in the afternoon, Alfonso Spagnolo came to notify me that Trombonicino had killed his wife with great cruelty for having found her at home alone in a room with Zoanmaria de Triomfo, who was seen by Alfonso at the window asking him [Alfonso] to find a ladder; but, hearing noise in the house, [Alfonso] did not wait and went inside. He found Tromboncino, who had attacked his wife with weapons, climbing the stairs accompanied by [his] father and a boy. Although he [Alfonso] reprimanded him, Tromboncino replied that he had the right to punish his wife [if he] found her in error, and, not having arms, he [Alfonso] was unable to stop him, so that when he returned home for arms, she was already dead. Zoanmaria, in the middle of this, jumped from the window. Tromboncino then retreated to [the church of] S. Barnaba with the father and the boy. For myself, I wanted to tell the story to Your Excellency and to beg you that, having had legitimate cause to kill his wife, and being of such goodwill and virtue as you are, to have mercy on them, and also on the father and the boy, who, as far as Alfonso could tell, did not help Tromboncino in any way except to escape…” (Source: Atlas, Aragonese 350).