He was again re-elected to be President of Colombia in 1886 and in 1892 but did not take office for his last term. He had moved back to Cartagena by then as his health deteriorated. Rather, his vice-president, Miguel Antonio Caro was sworn in as the de facto president for the presidential term of 1892-1898. While his contact with the central government was thus only indirect, Núñez remained an important political figure, and his letters and columns and essays were very influential. Moreover, many political figures of the time went to visit him constantly in Cartagena. His health continued worsening and he finally died on September 18, 1894, following a fever that left him in bed and speechless for a couple of days. Núñez died being officially appointed as president.