The king of Ormuz had fallen into arrears of life tribute, and was due 500,000 ducats, which he was unable to pay; for the tribute had been successively raised from 12,000 ducats originally imposed by Albuquerque, to 100,000, so that from a tributary he became a slave, not having even a competent maintenance remaining. Finding him unable to discharge the debt, De Sousa proposed to him to make over the customs of Ormuz to the Portuguese, which he agreed to, that he might get rid of the oppression. But the Persians soon afterwards deprived them of this source of revenue, which they had unjustly appropriated to themselves.

In the year 1544, De Sousa fitted out a fleet of 45 sail, in which were embarked 3000 seamen and soldiers. The design of this armament was kept a profound secret, which was to rob the pagoda of Tremele, 12 miles inland from St Thomas of Meliapour, in the kingdom of Bisnagar, for which express orders had been given by King John, under pretence that India was wasted, as if any pretence could justify robbery. The design was however discovered, or as others say it was disappointed by contrary winds. Yet the governor was persuaded to plunder other pagodas, where it was thought there were equal riches. By the way, he sent a message to the king of Jafnapatam in the island of Ceylon, commanding him either to become tributary to the crown of Portugal, or to prepare for opposing the armament. The king agreed to pay 4000 ducats yearly, glad to get off so easily. A king called Grande near Cape Comorin, being in fear of the Portuguese, sent a present to the governor. De Sousa proceeded to a pagoda named Tebelicate363, near Calecoulam, although the Portuguese were at peace with the king of that country, and went into it with a small number of his confidants, whence they brought out two casks so heavy that they loaded many men. These casks were reported to contain water, though some affirmed that it was gold and jewels; but the truth was never known. It has been alleged by some writers that nothing was found but a golden vessel worth 4000 crowns, in which the idol used to be bathed, and which was ordered to be restored by the king of Portugal, who was much displeased at the conduct of De Sousa on this occasion; as if it were a greater crime to rob the pagoda of Tebilicare without orders, than that of Tremele with orders. While the Portuguese were returning to their ships, the town and pagoda were set on fire, and they were attacked in a narrow defile by 200 Nayres, who killed 30 of them; but on getting into the open field, the Nayres were put to flight. No danger terrifies avarice. The Portuguese went on to another pagoda, from which a chest was brought out and opened publicly, and some silver money which it contained was distributed among the troops; but of so small account, that many believed the liberality was owing to that circumstance.

De Sousa was obliged to return in all haste to Goa, owing to the following circumstance, communicated to him by a message from Don Garcia de Castro. Aceda Khan, lord of the lands around Goa, intending to depose Adel Khan, prevailed on Don Garcia, by means of presents to deliver up to him Meale Khan the brother of Adel Khan, pretending that he held the kingdom wrongfully. This gave just cause of complaint to Adel Khan, and occasioned considerable danger to the Portuguese. The governor listened to the arguments and offers of both sides; but inclined more to favour Aceda Khan, who offered to cede the kingdom of Concan, giving a revenue of about a million, then possessed by Abraham, a good man and a friend of the Portuguese. As this territory was very valuable, particularly from its neighbourhood to Goa, the governor declared in favour of Meale Khan, and prepared to possess himself of the Concan which was offered by Aceda Khan. This was a notorious act of injustice; and as De Sousa was naturally of a haughty disposition, none of his officers dared to remonstrate; but Pedro de Faria, then four-score years of age, trusting to his quality and the great offices he had held, repaired late one night to the governors tent, and prevailed upon him to desist from so unjust an undertaking. Next day the governor abandoned his design, pretending various reasons of delay, and returned to Goa, carrying Meale Khan along with him.

At this time Aceda Khan died, who was the contriver of this discord, and Adel Khan descended the gaut mountains with a powerful army to reduce the rebels, recovering possession of the Concan in a few days. But as Adel Khan was still fearful of Meale Khan, he offered the lands of Salsete and Bardez to De Sousa, on condition of delivering him up, which were valued at 50,000 ducats of yearly revenue. De Sousa refused to give up this man who had confided in him for protection; but offered, if put in possession of these districts, that he would remove Meale to some place where he could give no disturbance to Adel Khan. These conditions were agreed to and performed by Adel Khan, but evaded by De Sousa, who sent Meale to Cananor and brought him back to Goa. Some alleged that this was done to overawe Adel Khan, while others said it was meant as a bait to extort presents; and it was certain that some were actually sent.

In this treaty, Adel Khan had agreed that De Sousa was to be put into possession of the vast treasures which had been left by the rebel Aceda Khan, said to amount to ten millions of ducats, and which at his death had fallen into the hands of Khojah Zemaz-oddin, who persuaded De Sousa that it was only one million, and delivered that sum to him. Adel Khan afterwards gave notice to De Sousa of the vast fraud which had been used in the pretended delivery of the treasure; but all his efforts to secure the defaulter were in vain.

Sultan Mahmud, sovereign of Cambaya or Guzerat, was desirous of recovering possession of the castle built by the Portuguese at Diu, and of freeing himself by that means from the trammels which had been thrown in the way of the trade of his dominions. In the late treaty between him and the Portuguese, it had been stipulated, with the consent of the viceroy Don Garcia, that the government of Cambaya might erect a wall between the city of Diu and the castle. This wall was accordingly commenced; but as Emanuel de Sousa, who commanded in the castle of Diu, considered that the wall now building was of a very different description from a mere boundary, as intended in the treaty, and appeared to be destined for hostile purposes, he drove away the workmen, threw down the wall, and made use of the materials for strengthening the defences of the castle. Mahmud was highly offended at this procedure, and at the instigation of his great minister Khojah Zofar, he secretly used every possible means to stir up enemies to the Portuguese, endeavouring to form an union of the Indian princes to expel them not only from Diu but from all India.

In the course of this year 1544, the great Khan of the Tartars invaded China and besieged Peking with a prodigious army, amounting to millions of men. A large detachment from this vast army, among which were 60,000 horse, was sent against the city of Quamsi, which was plundered, and an immense number of the inhabitants put to the sword. While on his return with this part of the army, Nauticor the Tartar general attempted to reduce the fortress of Nixiancoo, but was repulsed with the loss of 3000 men, on which he was disposed to desist from the enterprise, deeming the place impregnable. Among the prisoners taken at Quamsi were nine Portuguese, one of whom named George Mendez made offer to the Tartar general to put him on a plan for gaining the fortress of Nixiancoo, on condition that he and his companions were restored to liberty. The general agreed to his proposal, and gained the fort by the advice of Mendez, with the slaughter of 2000 Chinese and Moguls. In pursuance of his promise, the general obtained the liberty of the Portuguese from his sovereign, but prevailed on Mendez to continue in his service by a pension of 6000 ducats. The Tartar emperor was constrained to raise the siege of Peking and retire to Tuymican his residence in Tartary, after having closely invested the metropolis of China for almost seven months, with the loss of 450,000 men, mostly cut off by pestilence, besides 300,000 that deserted to the Chinese.