A first cousin of Parliamentarian general William Waller, he fought for Parliament in the Wars of the Three Kingdoms, becoming a leading member of the radical element within the New Model Army.

An admirer of Oliver Cromwell, Waller became a political and religious radical; he took part in the 1647 Putney Debates, supported Pride's Purge in December 1648 and was a judge at the Trial of Charles I in January 1649.

During the Protectorate, he held considerable political power in Ireland and was arrested in February 1660 after staging a coup in an attempt to prevent the Restoration of Charles II.

[5] These connections ensured that despite his conviction for regicide in 1660, the Waller family held onto their Castletown estates and remained significant figures in Munster society into the 20th century.

Protestants saw this as a threat, while many Confederates felt they were on the verge of victory and gained nothing from the truce; they were also well aware any concessions Charles made to Catholics in Ireland undermined his position in England and Scotland.

He transferred back to Ireland in February 1647 but fell out with Inchiquin and returned to England, where he became increasingly involved in radical politics and took part in the Putney Debates.

[1] During the 1648 Second English Civil War, he served as Parliamentarian commander in the strongly Royalist West Country and successfully suppressed a number of local revolts.

[10] Troops from his regiment took part in Pride's Purge in December which excluded moderate MPs from Parliament, while he was one of the 59 judges who signed the death warrant for the Execution of Charles I in January 1649.

One of only two regicides to plead guilty, he claimed to have been appointed to the trial without his knowledge, a suggestion dismissed by the republican Edmund Ludlow as indicating "one who would say anything to save his life".