However, the ongoing tensions between the two sides resulted in the outbreak of the First English Civil War in August 1642;Ormonde could no longer receive reinforcements or money from England, and by early 1643 the Confederacy held most of Ireland, with the exception of Ulster, Dublin and Cork City.
Alongside local Confederate forces they captured a series of Protestant-garrisoned towns notably Ballybeg where they seized a large quantity of supplies and Protestant hostages.
The plundering of the area by O'Neill's forces led to intense hostility from local Catholic inhabitants against the Ulster Army which was to become a recurring feature during the war.
O'Neill placed his troops in defensive positions near a ford over the river and around a nearby flour mill; he then led some of them forwards until they made contact with the enemy, then withdrew hastily in an effort to draw Moore's army onto unfavourable ground.
Although the victory brought an end the series of defeats that the Ulster Army had suffered over the previous two years, the defensive battle at Portlester gave little advantage to the Confederates as they lacked the resources to attempt a further advance eastwards towards Dublin.
Shortly afterwards a cessation of arms was agreed between the Dublin government of Ormond and the Irish Confederates as a first step towards negotiating a peace treaty and alliance against their mutual enemies the Roundhead forces in England.