In July 1922, with a command of 450 men, and an 18 pounder field gun, Prout re-took the city of Waterford from anti-treaty forces after a three-day battle (see Irish Free State offensive).

After a final stand at Redmondstown, the Anti-Treaty IRA in the south east gave up their fixed positions and took up guerrilla warfare.

A National Army report of October 1922 stated, "Prout is too weak as well as too guilless to handle traitorous or semi-mutinous incompetents".

In December a number of posts under Prout's command, including Carrick on Suir, surrendered to an anti-Treaty column under Tom Barry, giving up their arms and equipment.

Nevertheless, his command was criticised by National Army GHQ until after the end of the war for its performance – particularly for its failure to stamp out guerrilla activity in County Wexford.

"[11] Tipperary IRB centre Eamon O'Dwyer's witness statement to the Irish Bureau of Military History stated: "The civil war disgusted him and he has been back in the USA for many years.