Dom Constantino de Braganza's internal reforms resembled those of João de Castro; he endeavoured to put down peculation, and insisted on the obedience of his officers. In 1560 he made an expedition with a powerful armament to Ceylon, where he took Jaffnapatam, which became the capital of the Portuguese power in that island. The high character of the young prince, no less than his courage and his enterprise, caused the Rájás of India to treat him with great respect, and he was begged by the Queen Regent to continue in office, and even to accept the post of Viceroy of India for life. He refused, and in 1561 was succeeded as Viceroy by Dom Francisco de Coutinho, Count of Redondo.
After the resignation of Dom Constantino de Braganza few events of importance happened for some years to the Portuguese in India. The Muhammadan King of Bijápur, Ali Adil Sháh, who had succeeded his father Ibráhím in 1557, was at first more concerned with his scheme to break the power of the last great Hindu sovereign, the Rájá of Vijayanagar, than to attack the Portuguese. Freed from danger on this side, the Portuguese governors were able to scatter their power over small but successful expeditions. The most notable of these was to Ceylon, which was gradually brought entirely under the control of the Portuguese. The Count of Redondo died in March, 1564, at Goa, and was succeeded as Viceroy, after a short administration as Governor by João de Mendonça, by Dom Antão de Noronha.
The new Viceroy commenced his government by the capture of Mangalore, but the important events which occurred during his tenure of office took place without his active intervention. The first of these was the siege of Malacca by the King of Achin. The defence of Albuquerque's conquest ranks with that of Diu. It is true that the savage Achinese were not such formidable soldiers as the Turks or the Gujarátís; but, on the other hand, Malacca was further from Goa, and it was more difficult to obtain reinforcements. The Captain who maintained the defence was Dom Leonis Pereira, who held out for several months and eventually beat off his enemies after killing more than 4000 of them.
The other event was the defeat of the Rájá of Vijayanagar in 1565, at Tálikot, by the allied Muhammadan kings of the Deccan. It may fairly be conjectured that Albuquerque would have assisted the last powerful Hindu monarch against the Muhammadans, for it was a part of his policy to pose as the protector of the Hindus. But his successors did not appreciate his policy, and, disgusted by an attack which the Hindu prince had made some years previously on the Portuguese settlement of Saint Thomé, they left the Rájá of Vijayanagar to his fate.
In 1568 Dom Luis de Athaide, an officer who had had much experience in Indian warfare, and who had been knighted as a lad by Dom Estevão da Gama in the monastery of Mount Sinai, arrived in Goa as Viceroy. He quickly perceived that a first result of the victory of Tálikot must be that the King of Bijápur would attack Goa. The city of Goa had far outgrown the limits imposed by the wall which Albuquerque had built. Dom Antão de Noronha had, during his government, begun to build a new wall, which was to run from the north-eastern angle of the island of Goa and should terminate at the west of the city. Dom Luis de Athaide continued this wall, and was in the act of building other fortifications when Ali Adil Sháh declared war and made his way into the island with an army estimated at 100,000 men, and accompanied by more than 2000 elephants. This attack was part of a general scheme formed by the Muhammadan rulers of India, with the Zamorin of Calicut and the King of Achin, to expel the Portuguese from Asia. Even sovereigns who had hitherto been allies of the Portuguese, such as the Rájá of Honáwar, joined in the league against them.
Never was the situation of the Portuguese more critical; never did they show more conspicuous valour. The garrison of Goa, when the siege commenced in 1570, only consisted of 700 Portuguese soldiers. Consequently the Viceroy placed under arms 300 friars and priests and about a thousand slaves. The defence was worthy of the best days of the Portuguese power. For ten months an obstinate resistance was offered, and at the end of that time Ali Adil Sháh retreated, having lost by disease and by fighting the larger part of his army.
The defence of Goa, by the Viceroy, was rivalled by the gallant resistance of Malacca, of Chaul, and of Chalé near Calicut, where Dom Leonis Pereira, Dom Jorge de Menezes, and Dom Diogo de Menezes, all repulsed their assailants. On the retreat of Ali Adil Sháh from before Goa, the Portuguese Viceroy swept the Malabar coast, punishing all opponents and relieving the other garrisons. His vengeance was particularly shown at Honáwar, which he burnt. Just after the league was finally broken, on September 7, 1571, Dom Antonio de Noronha arrived to succeed Dom Luis de Athaide as Viceroy. The defender of Goa received a cordial welcome on his return to Lisbon from his friend, the young King Sebastian, who created him Count of Atouguia.
Dom Antonio de Noronha, who was only a distant relative of the predecessor of Dom Luis de Athaide, did not possess the powers of previous Viceroys. King Sebastian perceived the great inconvenience of leaving the whole of his possessions from the Cape of Good Hope to Japan under the superintendence of the Goa government. The difficulty of communication was so great that for months at a time the captains of the more distant settlements were practically independent. It was resolved, therefore, to divide the East into three independent governorships.