North Borneo, like the Philippines, had long been semi-civilized by intercourse with China. All well-to-do people possessed porcelain dishes and cups, and the Muhammadan Malays used bronze money impressed with Chinese characters. The Bornean Malays had a curious habit of taking small doses of mercury (quicksilver), not only to cure illnesses, but in the belief that it prevented sickness by purging the body. Pigafetta also relates that the Sultan of Brunei possessed two pearls as large as hens' eggs, so round, however, that they would not stand still on a table. These pearls came from the south-western islands of the Philippine archipelago. They had belonged to the king of the principal island of the Sulu archipelago, whose daughter had married the Sultan of Brunei, and had unwisely boasted of her father's pearls as big as hens' eggs. Her husband determined to get possession of them, by force if necessary, so had assembled a fleet of 500 praus (or, as another variant of the story puts it, 50), and sailing by night he surprised the King of Zolo, or Sulu, and two of his sons, and carried them off to Brunei, where he held them as captives until the pearls were delivered to him.

Pigafetta realized the immense size of the Island of Borneo—the second largest island in the world, only New Guinea being of greater area if Australia be considered a continent—he was informed that it took three months to sail round it in a Malay prau. It was a region that produced camphor,[35] cinnamon, ginger, myrobalans,[35] oranges, lemons, water-melons, cucumbers, gourds, and many other vegetables and fruits; buffaloes, oxen, swine, goats, fowls, geese (derived from China), deer, elephants, and horses.

After leaving Brunei the two ships directed their course towards the Sulu archipelago, which lies between North Borneo and Mindanao. They seem to have made little scruple of behaving like pirates towards any Malay prau which could not offer much resistance. In this way they captured a vessel full of coconuts, which was a great resource to them in the way of food. They found a perfect port for repairing ships in Bungei, one of the Sulu Islands. Here they stayed for forty-two days, everyone labouring hard, their greatest fatigue, however, being the journey backwards and forwards to the forest barefoot (probably because their shoes were worn out) to hew timber for the ship's needs. On the island of Bungei they found many wild boars (of the species Sus longirostris), with very long heads 2½ feet in length, and with big tusks. There were also huge crocodiles, and on the seashore immense Tridacna clam shells, the actual flesh of one of these clams (a clam is something like an oyster) weighing as much as 44 pounds. Here also they observed the marvellous leaf-insects, which Pigafetta not unnaturally imagined to be a miracle of nature, leaves which became alive and walked about when they fell to the ground. He kept one of these in a box for nine days, and at the end of that time the leaf-insect was still active, though no doubt it soon died, since he believed it fed on nothing but air.[36]

Stopping off the coast of the large island of Mindanao, the southernmost part of the Philippines, they again captured a Malay vessel (killing several of its seamen) apparently only for the purpose of getting information about the right course to pursue in order to reach the Spice Islands. From these captives they obtained, besides other information, the story that in the southern parts of Mindanao existed a race of hairy men who were fierce fighters and used bows and arrows with great effect. They also possessed swords or daggers, and when they were successful in battle they cut out the hearts of their slain enemies and ate them raw, seasoned with the juice of oranges or lemons. These hairy people were called Benaian.

Sailing away from Mindanao the two Spanish ships encountered a furious storm, and in their terror the crews lowered all the sails and offered up fervent prayers to God for their safety. "Immediately our three patron saints of San Nicolau, San Elmo, and Sta. Clara appeared to us like torches of light on the maintop, mizentop, and foretop.[37] We promised a slave each to St. Elmo, San Nicolau, and Sta. Clara, and offered alms to each saint." After this the storm abated and the ship found a welcome refuge in a harbour, where again they captured forcibly Malay seamen to show them the way to the Molucca Islands.

At last, on 8 November, 1521, they reached the five islands known as Maluk or Molucca, and on that date came to an anchor in a harbour of Tidore, where they fired a tremendous salute with their artillery. The next day the king of the island—evidently well used to Europeans and their ways—came off in a prau, and a deputation of Spaniards went in a small boat to meet him. They found him seated under a silk awning which sheltered him on all sides, and in front of him squatted one of his sons holding the royal sceptre, and on either side were persons with jars ready to pour water over his hands, while two others held gilded caskets filled with betel paste. The king bade the white men welcome, and said that he had dreamt some time ago that ships were coming to the Molucca Islands from remote parts, and from that assurance he determined to consult the moon, whereupon he had seen the ships coming. He then came on board; all kissed his hand and led him to the stern, where he was honoured with a red velvet chair and given a yellow velvet robe made after the Turkish fashion. The king professed his desire to become the most loyal friend and vassal of the King of Spain, and declared that henceforth his island would no more be called "Tadore" (or Tidore), but Castilla, because of the great love which he bore to the mighty sovereign of Spain.

This Malay chief of Tidore was a Muhammadan, about forty-five years old, well built, of royal presence, and much skilled in astrology. He was clad in a shirt of delicate white muslin, the ends of the sleeves embroidered in gold. Round his waist, and reaching to the ground, was a coloured cloth, while a silk scarf was wrapped round his head, and above it was placed a garland of flowers. He asked for a royal banner and a signature of Charles V, and he would then place his dominions, which included the Island of Ternate, under the direction of Spain. He would also load up the ships with cloves, so that they might return to Spain with good commerce.

Eight months previously a notable personage had died in the Island of Ternate, poisoned by the orders of this same King of Tidore. He was a Portuguese, Francesco Serr[~ao], who had been, curiously enough, a most intimate friend of Magellan, and who was apparently the brother of the Jo[~ao] Serr[~ao], or Juan Serrano, the commander of the Concepcion, who had been left behind and perhaps killed at Sebu. Francesco Serr[~ao] had been sent as captain of a Portuguese ship to the Moluccas in 1511, and had remained in those islands partly on account of disasters having happened to his ship. In course of time he became a very great man, and the Prime Minister, so to speak, of the King of Ternate. He had married a woman from the Island of Java. It was he who had strongly incited Magellan to attempt to reach the Moluccas by way of South America and the Pacific. But Serrano, having excited great jealousy by his powerful influence over the King of Ternate, was poisoned by this same King of Tidore, now so friendly towards the Trinidad and the Victoria; and soon afterwards the King of Ternate was likewise got rid of by means of poison, and so the monarch of Tidore was the chief person then in the archipelago of the Moluccas.

Whilst remaining at Tidore to load up with cloves, Pigafetta collected some information about the large island of Jilolo lying to the east.[38] He describes it as being inhabited both by Muhammadan Malays (on the coast) and by Papuan heathens (in the interior), and says it was very rich in gold, and that it grew enormous bamboos as thick round as a man's thigh, the segments of which were often filled with water that was very good to drink.