Born in the Republic of Genoa, in the 1470s Bartholomew was a mapmaker in Lisbon, the principal center of cartography of the time, and conceived with his brother the "Enterprise of the Indies", a scheme to reach the Orient and its lucrative spice trade by a western rather than an eastern route. In 1489 he went to England to seek assistance from Henry VII for the execution of the scheme. He was taken by pirates and landed in England in a destitute condition, and on presenting himself at Court was unfavorably received by the King. He then sought help at the court of Charles VIII in France, again without success. Meanwhile his brother Christopher was in Spain to persuade Isabella I of Castile and Ferdinand II of Aragon to back the scheme.
When word arrived in 1493 that his brother had succeeded, Bartholomew returned to Spain, where he missed Christopher, who had already left on the second voyage of his four to the "New World". Funded by the crown, Bartholomew Columbus traveled to Hispaniola in 1494 to meet his brother. After captaining one of the ships he remained on the island for six and a half years (1494–1500), serving as governor with the title of Adelantado during his brother's absences. He founded the city of Santo Domingo on Hispaniola between 1496 and 1498, which is now the capital of the Dominican Republic. He was imprisoned together with Christopher and another brother, Giacomo (also called Diego), by Francisco de Bobadilla and returned to Spain in December 1500. After the royal pardon of Christopher Columbus, Bartholomew Columbus accompanied him on the last of his New World voyages, where Bartholomew was to be left with a garrison near the Belén River. They were defeated by the local Ngöbe leader, el Quibían.
Following Christopher Columbus's death in 1506 Bartholomew returned to the Antilles, accompanying his nephew Diego, but Bartholomew soon returned to Spain when the king confirmed his concession involving Mona Island near Puerto Rico; the king would reclaim the appealing little island from Bartholomew's heirs after Bartholomew's death on 12 August 1514 (by which time Bartholomew had returned to Hispaniola).
Bartholomew Columbus is known to have fathered a daughter out of wedlock, named Maria and born in 1508.
- Augusto Mascarenhas Barreto: O Português. Cristóvão Colombo Agente Secreto do Rei Dom João II. Ed. Referendo, Lissabon 1988. English: The Portuguese Columbus: secret agent of King John II, Palgrave Macmillan, ISBN 0-333-56315-8