A prominent member of Protestant society in Munster during the 1630s, Waller fought against the Catholic Confederacy following the 1641 Irish Rebellion. When the First English Civil War began in August 1642, Charles I wanted to use his Irish troops to help win the war in England, and in September 1643 agreed a truce or "Cessation" with the Confederacy. Waller opposed this and defected to the Parliamentarians; in April 1645, he was appointed a Colonel in the New Model Army and fought throughout the final campaigns of 1645 and 1646.