In 1567 he was arrested at the instance of Thomas Francis, president of the London College of Physicians, for practising medicine without license of the college. He was lodged in the King's Bench prison, and 27 May 1567 he wrote to Cecil asking for an opportunity to expose Francis's ignorance of astronomy and Latin; and petitioned for his release. and for financial assistance. On 3 May 1568 he supplicated at Oxford for incorporation as a doctor of medicine of Cambridge. Early in 1569 Bomelius's wife stated before the council of the College of Physicians that her husband had given due satisfaction for his offence to the queen and the lord treasurer, and petitioned for the council's consent to his liberation. The council demanded payment of a fine and costs, which Bomelius's poverty did not allow him to pay. On 2 June 1569 the council appears to have offered Bomelius his release on condition of his giving a bond to abstain henceforth from the practice of medicine; but early in 1570 he would seem to have been still a prisoner, and his wife was in frequent communication with Archbishop Matthew Parker as to the conditions of his release. Before Easter 1570 Bomelius was an "open prisoner" of the King's Bench, and in April 1570 Parker was intending to take a bond from Bomelius to leave the country. Bomelius diverted this outcome by announcing in a letter to Parker that he had knowledge of a terrible danger hanging over England. The archbishop sent the letter to Cecil and urged him to examine Bomelius in the privy council. But Cecil entered into private correspondence with the doctor in the expectation of discovering a conspiracy. What Bomelius communicated to Cecil was a statement on the queen's nativity, and a portion of a book "De Utilitate Astrologiæ", in which he claimed that great revolutions take place every 500 years, and that as rather more than 500 years had elapsed since the Norman conquest, England must be in imminent peril. Cecil treated Bomelius's announcements as worthless. Russian ambassador Andrei Sovin, who was in London at the time, offered to take Bomelius to Russia. The English government did not hinder his departure, and late in 1570 Bomelius, who had promised to supply Cecil with political information and to send him small presents yearly, was settled in Russia. When Sir Jerome Horsey began his travels in 1572, he frequently met Bomelius at Moscow, and he wrote that Bomelius was then living in pomp at the court of Ivan the Terrible.