On 21 November 1920 (Bloody Sunday (1920)) Cooney was one of the Volunteers who shot six British Army Intelligence officers (three were killed) at 28 Upper Pembroke Street, Dublin.
He opposed the Anglo-Irish Treaty of 1921 and in March 1922 was appointed Commandant of the 1st Eastern Division of the anti-Treaty IRA in the Irish Civil War.
He accepted responsibility for an attempted escape bid on 10 October 1922 in which a fellow prisoner Peadar Breslin was killed and another man was wounded.
He succeeded Frank Aiken as Chief of Staff of the IRA in 1925; after eight months in that role, he departed on a fund-raising trip to the United States, but soon returned.
Thereafter, semi-retired from active republicanism, he continued to be a regular orator at gatherings, and he was a founder of the short-lived Cumann Poblachta na hÉireann party in 1936.