On 7 January 1922 the Anglo-Irish Treaty was approved by the Second Dáil by a close vote of 64–57. On 5 February a convention was held to discuss this, and 419 Cumann na mBan members voted against as opposed to 63 in favour. In the ensuing Civil War, its members largely supported the anti-Treaty Republican forces. Over 400 of its members were imprisoned by the forces of the Provisional government which became in December 1922 the Irish Free State. Some of those who supported the Treaty changed the name of their branches to Cumann na Saoirse, while others retained their name but gave allegiance to the Free State Government.

Cumann na mBan continued to exist after the Treaty, forming (alongside Sinn Féin, the Irish Republican Army, Fianna Éireann and other groups) part of the Irish republican milieu. The government of the Irish Free State banned the organisation in January 1923 and opened up Kilmainham Gaol as a detention prison for suspect women.

Its membership strength was adversely affected by the many splits in Irish republicanism, with sections of the membership resigning to join Fianna Fáil, Clann na Poblachta and other parties. Máire Comerford, a lifelong member from 1914, reflected in later years that it became a ‘greatly weakened organisation’ that ‘gathered speed downhill’ from the founding of Fianna Fáil in 1926.