Clifford was a man of irregular life, and having run through a great part of his very handsome property, seized on the opportunity offered by the war with Spain to re-establish himself. In 1588, he commanded the galleon "Elizabeth Bonaventure" in the Anglo-Spanish War, during which he had had some success. He led and invested in a number of expeditions, but many were turned back due to storms or lack of prizes. His first success was an expedition to the Azores in 1589, taking a number of Portuguese and Spanish prizes. He suffered losses in the Battle of Berlengas Islands in 1591, and in 1592 he helped to prepare an expedition with Walter Raleigh, which led to the Battle of Flores, and the capture of the richly laden Portuguese ship, Madre de Deus, off Flores Island in the Azores. At the end of 1593, Clifford financed three ships for a further expedition to the Azores, which resulted in the Action of Faial between the English and a joint Iberian/Portuguese fleet.