He left Rotterdam on 2 July 1598 with four ships to find an alternative trade route to China and the Spice Islands during the Dutch Eighty Years' War with Spain and Portugal.

Van Noort sailed through the Strait of Magellan, and captured a number of Spanish and Portuguese ships along the Pacific coast of South America.

[1] In November and December 1600, he established a berth for his two remaining ships, Mauritius and Eendracht, in the surroundings of Corregidor Island at Manila Bay in the Philippines.

The Spanish lost their flagship, the galleon San Diego (its wreck would be found in 1992 and yield a treasure in porcelain and gold pieces) but the Spanish captured the Dutch Eendracht, making van Noort's position untenable and forcing him to retire from the Philippines.

Van Noort returned to Rotterdam via what would become the Dutch East Indies and the Cape of Good Hope, on 26 August 1601 with his last ship, the Mauritius, and 45 of the original 248 crew.