Botello immediately landed and gave the necessary orders and again embarking forced his way up the river through showers of bullets, which he repaid with such interest that the enemy abandoned their advanced works that same night, and retired to that which they had constructed on the ruins of the Capuchin monastery. As the river Pongor had not sufficient water for the Portuguese ships, Botello embarked a strong detachment in 33 balones or balames, being country-vessels of lighter draught, with which he went in person to view the strength and posture of the hostile fleet. Being anxious for the safety of their gallies, the enemy abandoned their works at Madre de Dios and San Juan, and threw up other works with wonderful expedition for the protection of their fleet. But having attacked these with much advantage, Botello proposed to the enemy to surrender, on which Marraja returned a civil but determined refusal. His situation being desperate, Marraja endeavoured the night to escape with the smaller vessels, leaving his large gallies at the mercy of the Portuguese, but was prevented by the vigilance and bravery of Vasquez de Evora, who cut off many of his men, not without some loss on his own side, having one of his arms carried off. The enemy now endeavoured to make use of their formidable gallies, and the chief among them called the Terror of the World was seen in motion; on which Botello sent the admiral of the Portuguese gallies, Francisco Lopez to attack her, which he did with great gallantry, passing through clouds of smoke, and a tremendous fire of artillery, and after two hours hard fighting, carried her by boarding, after killing 500 of her men out of 700, with the loss only of seven of his own men.

On the 25th of November, the enemy set fire to a galley that was full of women whom they had brought to people Malacca, and made a fresh attempt to break through the Portuguese fleet, but without success, many of them being slain and taken, and great numbers leapt into the water, and fled to the woods, where they were devoured by wild beasts. Lacsamana then hung out a flag of truce, and sent a deputation to treat with Botello, who answered that he would listen to no proposals till they restored Pedro de Abren the Portuguese ambassador, whom they kept prisoner; and as they delayed compliance; the Portuguese cannon recommenced a destructive fire. On the last day of November, Botello got notice that Marraja the Acheen admiral was slain, and that the king Pam was approaching to the assistance of the Portuguese with 100 sail of vessels. Botello went immediately to visit him, and was received with the customary ceremonies used by the eastern princes to the Portuguese governors. After interchanging presents and mutual compliments, Botello returned to his post, where he found the Portuguese rather slackening their efforts in consequence of a desperate cannonade from the enemy. But on the 4th of December, the enemy sent fresh proposals for an accommodation, accompanied by the ambassador Abreu, requiring only to be allowed to withdraw with three of their gallies and 4000 men, being all that remained of 20,000 with which they had invested Malacca. In answer to this, they were told they must surrender at discretion on promise of life; and as Lacsamana hesitated to accept such humiliating terms, Botello assaulted and forced all his works, where many of the enemy were put to the sword; some throwing themselves into the river to swim across were drowned, and others who fled to the woods were devoured by beasts of prey. In fine, Botello obtained the most glorious victory that was ever gained by the Portuguese in India; as of all the fleet which came against Malacca, not a single vessel got away, and of the large army, not one man escaped death or captivity. So great was the booty, that the whole of the Portuguese troops and mariners were enriched, Botello reserving nothing to his own share but a parrot which had been much valued by Lacsamana.

On going to Malacca after this great victory, he entreated to be allowed to walk barefooted and unaccompanied to church, that he might humbly prostrate himself before the Lord of Hosts, in acknowledgement that the victory was entirely due to God, and not to the Portuguese valour; but he was constrained to enter the city in triumph. The streets were crowded with men, and the windows and house tops thronged with women, who sprinkled the hero with sweet waters and strewed flowers in his path. The music could not be heard for the noise of cannon, and all the city was filled with extreme joy. At this time an embassy came from the king of Pera, who was tributary to the king of Acheen, offering to pay tribute to the king of Portugal, and to deliver up a large treasure left in his custody belonging to the king of Acheen and his general Lacsamana. Don Jerome de Silveyra was sent with eleven ships to receive the treasure, and establish a treaty with the king of Pera, who performed his promise, and the treasure was applied to pay the men and refit the fleet.

About the middle of January 1630, Botello being off the straits of Cincapura to secure the ships expected from China against the Hollanders, Lacsamana and two other officers who had fled to the woods were brought prisoners to him, having been taken by the king of Pam. Owing to contrary winds, he was unable to get up with five Dutch ships that were about Pulo Laer, and which took a Portuguese galliot coming from China. He returned therefore to Malacca to refit his ships, and resolved to attempt the Dutch fort of Jacatara20, the best which was possessed by these rebels in all Asia. In the first place, he sent Antonio de Sousa Coutinno in the admiral galley lately belonging to Lacsamana called the Terror of the World, in which Lacsamana was now prisoner, to Goa; directing that Lacsamana should be sent to Portugal, and that this large and magnificent galley should be given as a present to the city of Goa. In this galley there was one cannon made of tombac, a precious sort of metal, which was valued at above 7000 ducats, and another cannon reckoned still more valuable on account of its curious workmanship. Lacsamana died before he could be carried to Portugal.

Learning that the Count de Linnares, now viceroy of India, had arrived at Goa in October 1629, Botello transmitted to him an account of all that he had done, and desired his assistance and approbation to continue in these parts in order to carry on his designs against the English and Hollanders. About the end of April 1630, the viceroy not only sent him every thing he asked, but gave him full power to act as governor general, without being obliged to wait for orders from Goa. In the meantime Botello sailed with 27 ships towards the straits of Cincapura, and put in at Jambo21, a place abounding in pepper, and on that account much resorted to by the Dutch and English. At this place he took two large ships after a stout resistance; and going higher up the river he discovered another ship so large and beautiful that he designed to make use of her for his entrance into Goa; but a ball falling into her powder-room, blew her up. After employing three weeks in working up the river, Botello learnt that at a town about two leagues distant, two Dutch ships had taken shelter, and being desirous of taking them, he manned 14 light vessels with which he went to view the place, on which he was opposed by 26 sail of small vessels manned with Hollanders and natives, whom he put to flight; but on viewing the place he found it impracticable to attempt the two vessels, on account of the strength of the works by which they were protected. He destroyed therefore all the neighbourhood with tire and sword, and then sailed down the river, intending to proceed against Jacatara.