Carew was appointed President of Munster on 27 January 1600, at the height of the Nine Years War and landed with Lord Mountjoy at Howth Head a month later. He enjoyed wide powers, including imposition of martial law, and excelled in the politics of divide and rule. He interviewed the successor to the Earl of Clancarty, Florence MacCarthy, in the spring of that year, after an unjust attack by presidency forces on the MacCarthy territories prior to his arrival. He was present as a guest when the Earl of Ormond was seized by the O'Mores at a parley in the same year, and managed to escape with the Earl of Thomond through a hail of daggers. At about this time he put down the supporters of the Súgán Earl of Desmond, and in October the lawful Desmond heir, James FitzGerald, was restored to the title in a limited degree. In August, Carew had accepted a reinforcement of 3,000 troops from England, but in the following May was dismayed when Mountjoy took 1,000 from him to supplement the crown army in its northern campaign, at a time when the threat of a Spanish landing in the south was at its highest.