Born in Genoa in the 1461, Bartholomew became a mapmaker in Lisbon, the principal center of cartography of the time, and conceived with his brother the "Enterprise of the Indies", a planned expedition to reach the Orient and its lucrative spice trade by a western rather than an eastern route.

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".

He was imprisoned together with Christopher and another brother, Giacomo (also called Diego), by Francisco de Bobadilla and returned to Spain in December 1500.

The Europeans looted whatever took their interest from amongst the cargo and seized the elderly captain to serve as an interpreter; the canoe was then allowed to continue on its way.

Bartholomew Columbus had a natural daughter named Maria born in 1508 as the result on a relationship with Catalina Marrón.