Due to the threat of punishment and the potential scrutiny he feared from his peers within the scientific community, Newton may have deliberately left his work on alchemical subjects unpublished. Newton was well known as being highly sensitive to criticism, such as the numerous instances when he was criticized by Robert Hooke, and his admitted reluctance to publish any substantial information regarding calculus before 1693. A perfectionist by nature, Newton also refrained from publication of material that he felt was incomplete, as evident from a 38-year gap from Newton's conception of calculus in 1666 and its final full publication in 1704, which would ultimately lead to the infamous Leibniz–Newton calculus controversy.
Most of the scientists manuscript heritage after his death passed to John Conduitt, the husband of his niece Catherine. To evaluate the manuscripts, physician Thomas Pellet was involved, who decided that only "the Chronology of Ancient Kingdoms", an unreleased fragment of "Principia", "Observations upon the Prophesies of Daniel and the Apocalypse of St. John" and "Paradoxical Questions Concerning the Morals and Actions of Athanasius and His Followers" were suitable for publication. The remaining manuscripts, according to Pellet, were "foul draughts of the Prophetic stile" and were not suitable for publication. After the death of J. Conduitt in 1737, manuscripts were transferred to Catherine, who unsuccessfully tried to publish theological notes of her uncle. She consulted with Newtons friend, the theologian Arthur Ashley Sykes (1684–1756). Sykes kept 11 manuscripts for himself, and the rest of the archive passed into the family of Catherines daughter, who married the John Wallop, Viscount Lymington, and was then owned by the Earls of Portsmouth. Sykes documents after his death came to the Rev. Jeffery Ekins (d. 1791) and were kept in the family of the latter until they were presented to the New College, Oxford in 1872. Until the mid-19th century, few had access to the Portsmouth collection, including David Brewster, a renowned physicist and biographer of Newton. In 1872, the fifth Earl of Portsmouth transferred part of the manuscripts (mainly of a physical and mathematical nature) to Cambridge University.
In 1936, a collection of Isaac Newtons unpublished works were auctioned by Sothebys on behalf of Gerard Wallop, 9th Earl of Portsmouth. Known as the "Portsmouth Papers", this material consisted of 329 lots of Newtons manuscripts, over a third of which were filled with content that appeared to be alchemical in nature. At the time of Newtons death this material was considered "unfit to publish" by Newton's estate, and consequently fell into obscurity until their somewhat sensational reemergence in 1936.
At the auction many of these documents, along with Newtons death mask, were purchased by economist John Maynard Keynes, who throughout his life collected many of Newtons alchemical writings. Much of the Keynes collection later passed to eccentric document collector Abraham Yahuda, who was himself a vigorous collector of Isaac Newton's original manuscripts.
Many of the documents collected by Keynes and Yahuda are now in the Jewish National and University Library in Jerusalem. In recent years, several projects have begun to gather, catalogue, and transcribe the fragmented collection of Newtons work on alchemical subjects and make them freely available for on-line access. Two of these are The Chymistry of Isaac Newton Project supported by the U.S. National Science Foundation, and The Newton Project' supported by the U.K. Arts and Humanities Research Board. In addition, The Jewish National and University Library has published a number of high-quality scanned images of various Newton documents.