Gormanston in Meath, while by his marriage to Margaret, daughter and heiress of Walter de Bermingham, he acquired large estates in Leinster. He was appointed baron of exchequer in Ireland in 1365, and was subsequently keeper of the great seal in that country (Patent and Close Rolls, Ireland; Gilbert, Viceroys of Ireland, and Chartularies of St. Mary's Abbey, Dublin, 1884; Lodge, Peerage, i. 82; notes furnished by J. T. Gilbert, esq.).
Thomas was educated in the Spanish Netherlands, where he took service with the archdukes. Both he and Owen Roe O'Neill [q. v.] were captains in Henry O'Neill's Irish regiment at Brussels in July 1607 (State Papers, Ireland). Between Preston and Owen Roe was from the first a strong antipathy, which became embittered in the course of time by professional rivalry in the Spanish service (Gilbert, Confederation and War, iii. 3). Preston was in Ireland recruiting in 1615, and again in 1634, and Wentworth allowed him to recruit his regiment up to 2,400 men. Both Preston and O'Neill continued to draw men from Ireland until 1641, and their recruiting agents frequently came into conflict. From 24 June to 4 July 1635 Preston distinguished himself in the defence of Louvain against the combined forces of France and Holland, and sent to Wentworth an account of the exploit on 6 July 1635. In the summer of 1641 Preston threw himself into Genappe, of which he was made governor, and, after a gallant defence, capitulated to Frederick Henry of Orange in person on 27 July. In 1642 his nephew, Lord Gormanston, urged him to return to Ireland, and, resolving to sacrifice his hopes of promotion abroad, he prepared to join the Irish catholics in their rebellion against the English government.
Though Richelieu did not wish to appear openly in support of Irish rebels, he discharged all the Irish soldiers in the French service, so as to set them free for their own country, let it be understood that they might expect money up to a million crowns, and allowed war material to be purchased in France. Preston was at Paris in July 1642 (ib. ii. 67), and probably obtained a substantial subsidy in money. But he had married a Flemish lady of rank, and had more influence and interest in the Spanish Netherlands. It was accordingly from Dunkirk that he sailed with three armed vessels, carrying many guns and stores and a number of officers trained in continental warfare. He arrived in Wexford harbour at the end of July or beginning of August (Gilbert, Contemporary Hist. i. 519). At Wexford he was joined by a dozen of more vessels laden with munitions of war from Nantes, St. Malo, and Rochelle (Carte). Preston reconnoitred Duncannon fort, which he thought could be taken in fifteen days, and then went to Kilkenny, where the Catholic Confederation was established. He accompanied Castlehaven in his expedition against Monck, who had just relieved Ballinakill in Queen's County. Preston, by Castlehaven's account, pursued Monck, forced him to fight, and routed him near Timahoe on 5 Oct. Preston was formally chosen general of Leinster by the supreme council (14 Dec.) His first success was the capture of Birr Castle on 20 Jan. 1642–3 (Confederation and War, ii. 145). It had held out since the beginning of the war. The terms were honourable and were honourably kept. Castlehaven, who served under Preston, records with pride that ‘he delivered [the inmates of the castle], being about eight hundred men, women, and children, with their baggage, safe to their friends’ (p. 34). On 18 March 1642–3 Preston was totally defeated by Ormonde, near New Ross. Preston's forces were nearly two to one; but Castlehaven, who was present and a good judge, says he ‘put himself under as great disadvantage as his enemy could wish.’ Ballinakill was taken by Preston some weeks later, and Castlehaven escorted the defenders to a place of safety. In June 1643 Preston threatened the garrison of Castlejordan in Meath, but was foiled by Ormonde, and his operations during the summer were unimportant. On 15 Sept. the cessation of arms for a year between Ormonde and the confederates was concluded at Sigginstown in Kildare (cf. Confederation and War, iii. 3). Many soldiers went to England at the cessation, and few returned. When the year had expired there was a succession of short truces, during which abortive negotiations for peace went on.
After Lord Esmond, governor of Duncannon fort, declared for the parliament, the towns of Waterford and Ross, who feared to lose their trade, provided funds for its reduction. Preston began the siege on 20 Jan. 1644–5, and the fort was surrendered on 19 March. According to the diary of the Franciscan Bonaventure Baron, who was present (ib. iv. 189), 176 shells and 162 round shot were fired by the assailants; Carte adds that 19,000 pounds of powder were burned. But only thirty of the garrison were killed or died; famine and want of water were the real captors. The garrison were allowed to march out ‘with bag and baggage’ (ib. p. 184), and to be conveyed safely to Youghal or Dublin. But the forces of Preston and the confederates were unequal to the army which the parliament was collecting against them, and Preston's pecuniary resources were failing.