On 6 August 1562 he was found guilty of coining, and, with three of his associates, was condemned to death; he was, however, reprieved on consenting to serve under Ambrose Dudley, 3rd Earl of Warwick, in France.
After the death of Shane O'Neill in 1567 he was stationed at Carrickfergus in order to assist Captain Piers in keeping the Scots of the Glynns in check.
He was reproved by the lords justices for distraining Brian MacPhelim O'Neill's and other Irishmen's cattle for cess, but his conduct was justified by Sir Henry Sidney.
His position was a difficult one, and he complained that he had to feed his men at his own cost, but he displayed tact in his management of Sorley Boy MacDonnell, and Sidney, on visiting the north in October 1568, found the charge committed to him in very good state.
In the spring of 1571 he visited England, where he advocated colonising the north of Ireland with Englishmen to prevent the growth of a Scottish power.
On 5 October 1571 he obtained a grant of MacCartan's country, corresponding to the barony of Kinelarty in County Down, on condition that he planted it with civil and loyal subjects before 28 March 1579.
On 10 April he received a commission to execute martial law in MacCartan's country, but the indiscretion of Thomas Smith in publishing his scheme for the plantation of the Ardes and Upper Clandeboye, by putting the Irish on their guard, placed obstacles in the way of realising his plan.
He accompanied Sir Henry Sidney into Connacht in September 1576, and having been knighted by him on 7 October, was appointed colonel, or military governor, of the province (called Connaught by the English).
During his absence in England his officers and soldiers behaved badly, but Connacht remained tranquil; on the outbreak of James Fitzmaurice's Second Desmond Rebellion in July, Malby, with six hundred troops, marched to Limerick to co-operate with the lord justice, Sir William Drury.
He belonged to the Leicester faction, and for this and other more personal reasons bore no goodwill to Ormonde, whom he subsequently charged with misrepresenting his services in Munster, and with abetting disorder in Connacht.
O'Rourke fled at his approach; but John and Ulick Burke, at the instigation of the catholic bishop of Kilmacduagh, had proclaimed a religious war, and were making efforts to relieve the Spanish at Smerwick.
Towards the end of February a body of six hundred Scots invaded the province to co-operate with the Burkes, but Malby had notice of their arrival, and drove them across the Moy River.
Malby complained that the order forbidding him to raise men by cessing them on the country rendered him powerless to meet this danger.