In 1694, he retired from the University. His final years were marked by even more financial and personal troubles. He became ill, with what physicians identified as either gallstones or kidney stones and he was in considerable pain. His patron the Archbishop Aguiar y Seijas died and Sigüenza lost his lucrative post of Chief Almoner. He also lost the position of University Accountant. The death of his patron the Archbishop was clustered with the death of Sigüenza's father and favorite brother. His dear friend Sor Juana Inés de la Cruz died and he delivered the eulogy at her funeral. In November 1699, Sigüenza was named "corregidor general" (book examiner) for the Inquisition, a position that paid little and which took up considerable time vetting books for possible heresy.