Born in Cadiz to an Italian father and Spanish mother, Carlos went to sea at the age of 13. He was based in the Philippines and built up his experience on the route between Manila and Macao until he became a full captain in 1841. By February 1844 he had bought his own 146 ton topsail schooner, Il Martiri de Tunkin, and set out to find and salvage a valuable cargo from the wreck of the Christina, which had been reported in July 1842. He succeeded, surrendered (after some delay) the treasure to its insurers in Hong Kong, and was well rewarded.
Having undertaken several voyages in the islands south and east of the Philippines during which he freed several slaves and did some evangelising he became more interested in missionary work and went back to Europe for support and training. In 1855 he was appointed Priest Apostolic to Borneo by the Pope and left for the east in 1856 with two Italian priests to assist him.
The mission was welcomed in Labuan in 1857, and also established stations in Brunei and at Looc Porin (near where Kota Kinabalu is now). However, problems with his assistants left him alone from 1860 and the mission made little progress.
Cuarteron, already ill, resigned his post in Rome in December 1879, then returned to his sister's home in Cadiz, where he died of pneumonia on 12 March 1880.