In 1604 he went to the East Indies with his brother Henry, as second captain of the Red Dragon, and is mentioned as having conducted the negotiations with the native kings of Ternate and Tidore.
Middleton reluctantly proceeded without Keeling, and after touching in St. Augustine's Bay, arrived on 14 November at Bantam, whence after refitting he sailed for the Moluccas or Spice Islands.
He managed, however, to do business privately, and when the permission was withdrawn, within a few days of its being granted, he went to Bangay, and afterwards to Button, where he was well received by the king, and obtained a full cargo of cloves.
Middleton was recognised as a capable and fortunate commander, and was sent out again on the fifth voyage[2] in a larger ship, the Expedition, in which he sailed from the Downs on 24 April 1609, Davis being again his pilot master.
A month later he came to Button, where he entertained the king at a banquet on board; but no trade was to be done, owing to the recent destruction of the storehouses by fire, and he passed on to Bangay.
Foul winds compelled him to bear up for Banda, but there the Dutch governor told him plainly that to permit him to buy a nut there was more than his head was worth.
He names, too, his brother Christopher, his sisters and their children, several cousins and friends, the bulk of his property being left to his son Henry.