In 1587 she became the flagship of Sir Francis Drake and his squadron organized to combat the Spanish Armada. In action from 31 Jul 1588, she and the other English ships harried the Spanish fleet up the English Channel. On 1 Aug Drake broke off to capture the Nuestra Senora del Rosario, flagship of Don Pedro de Valdes and the Andalusian squadron, and greatest prize of the campaign. Drake rejoined the main English fleet and its continuing chase as the Spanish first took refuge in Calais, and then were driven out by fireships. On 8 Aug Revenge briefly engaged with Medina Sidonia's flagship San Martin and then chased the Spanish into the North Sea before putting into the Firth of Forth on 12 Aug for supplies.

The next year Revenge was again Drake's flagship in the unsuccessful expedition to Portugal. In 1590 she was the flagship of Sir Martin Frobisher in a failed attempt to intercept the annual Spanish treasure fleet. In Aug 1591 she was part of Lord Thomas Howard's fleet, flying the flag of Sir Richard Grenville, out searching for the Spanish flota when they were surprised on 8 Sep near Flores in the Azores by a Spanish relief fleet. While most of the English slipped away, Grenville stayed to fight and Revenge was surrounded and boarded by five Spanish ships, two of which eventually sank. After a fourteen hour battle the English surrendered; Grenville was mortally wounded and Revenge was so seriously damaged, she sank a few days later when a major storm caught the Spanish fleet before they could reach port.