De Goes was a native of Villa Franca do Campo in the Azores. As a young solider in India, he visited a chapel along the Travancore coast and decided to enter the Society of Jesus as a coadjutor brother. He studied Persian and accompanied Jerome Xavier to visit Akbar (r. 1556-1606), the Mogul ruler in Agra, in northern India, There the Jesuits, interested in a land route from India to China via central Asia, learned that a Muslim merchant had recently traveled overland to Khanbaliq (Peking), the capital of Cathay.
With letters of introduction from Akbar, de Goes and several companions joined a caravan that left Agra in October 1602, crossed the Pamirs (the high altitude region in the northwest corner of India), and reached Yarkand (now Shache), in western Sinkiang, which was then the capital of the kingdom of Kashgar. With a new caravan, he went on to Aksu and Sucha (Kuqa) in November 1604. At Yen-ch'i (Yanqi) he met a Muslim merchant who had lived with Matteo Ricci in a hostel for foreigners in Khanbaliq. Convinced that Cathay and China were identical, Goes and a few companions went on their own via Turfan (Turpan) and Hami and entered Suchow (now Jiuquan), Kansu (Gansu) Province, in late 1605. In reply to a letter from de Goes, Ricci sent a Jesuit brother, Chung Ming-li, who arrived less than two weeks before de Goes died.