In his will he had divided his estate between his two sons. Alexander inherited the Barony of Glenarm, whereas the elder, Randal, inherited the title and the larger share of the land, consisting of the baronies of Dunluce and Kilconway. Alexander was precisely 15 at that time. In his time children came of age at fifteen and he therefore entered immediately into the possession of his part of the estate. He made Glenarm Castle on the east coast of County Antrim his residence. The date of his first marriage does not seem to be known. He married, firstly, Elizabeth Annesley, second daughter of Arthur Annesley, 1st Earl of Anglesey, a Protestant. She died childless on 4 September 1672. After coming of age, Alexander MacDonnell spent three years travelling abroad in Europe on his grand tour. He returned to Ireland just before the outbreak of the Irish Rebellion of 1641, in which he sided with the rebels and commanded a regiment. Colonel Alexander MacDonnell, as he now was, led the regiment throughout the Irish Confederate Wars until the Confederation surrendered to Cromwell in 1652. Unlike his brother Randal, Alexander respected and adhered to the peace between the Confederates and the Royalists negotiated by Ormond in 1648 and urged for a conciliatory approach. His lands were confiscated in 1652 in Cromwell's Act of Settlement and distributed among Cromwellian soldiers. In exchange he received 3,500 acres in Connacht. By 1656, he was living in England. At the Restoration in 1660, he was appointed custos rotulorum for Antrim. In 1668 Alexander MacDonnell was restored to his lands by Charles II. He married, secondly, Helena Burke, daughter of Sir John Burke of Derrymaclaughna (Doire-mic-Lachtna), County Galway, after 1672. He had two children from his second wife:  On 3 February 1683 his only brother, Randal, died childless. Randal had married twice but both marriages were childless. The marquessate became extinct and Randal was therefore the first and last Marquess of Antrim of the 1645 creation. Alexander succeeded him in the earldom as the 3rd Earl of Antrim. In 1685, Lord Antrim, as he was now, was invested as a Privy Counsellor and Lord-Lieutenant of Antrim shortly after the accession of King James II, as the King followed a policy of replacing Protestant officials with Catholic ones throughout Ireland.