Indonesia's independence was proclaimed while Mongisidi was in Makassar. However, the Dutch sought to regain control of Indonesia after the end of World War II. They returned through the Netherlands Indies Civil Administration (NICA). Mongisidi became involved in the struggle against NICA in Makassar. On July 17, 1946, Mongisidi with Ranggong Daeng Romo and others formed the Indonesian people's resistance army in Sulawesi (), which continually harassed and attacked Dutch positions. He was caught by the Dutch on February 28, 1947, but managed to escape on October 27, 1947. The Dutch caught him again and this time sentenced him to death. Mongisidi was executed by firing squad on September 5, 1949. His body was moved to the Makassar heroes cemetery on November 10, 1950.