1536–1552: the Colegio de Santa Cruz opened at Tlatelolco in 1536. De la Cruz composed or dictated the medical material, Badiano translated it into Latin, and unnamed collaborators made the painted volume. The colophon dates completion to the feast of Mary Magdalene, 22 July 1552.
1552 and after: Francisco de Mendoza took the manuscript to Spain for the royal court. Accounts often place it immediately in the royal library or El Escorial, but the detailed chain of possession is not continuous enough to treat every transfer as certain.
By 1626: an ownership inscription connects the book to Diego de Cortavila y Sanabria, an apothecary to Philip IV. During Cardinal Francesco Barberini's Spanish legation in 1626 it passed into Barberini hands. A seventeenth-century copy made in the circle of Cassiano dal Pozzo's “Paper Museum,” now in the Royal Library at Windsor, demonstrates limited learned circulation in Rome without proving broad medical adoption.
1902–1940: the Barberini library entered the Vatican Library in 1902. Charles Upson Clark drew scholarly attention to the manuscript in 1929; saying that he “discovered” it exaggerates a modern research encounter into an act of creation. William Gates issued an English version in 1939, and Emily Walcott Emmart's 1940 colour facsimile, Latin transcription, translation and commentary made the manuscript far more accessible. Her title, The Badianus Manuscript, also helped centre the translator's name over De la Cruz's authorship.
1990–present: Pope John Paul II returned the manuscript to Mexico, where a public presentation was held at the Museo Nacional de Antropología on 15 July 1990. The holding institution's current catalogue instead dates the return to 1991, and Viesca's 1995 article says mid-1992; the documentary record therefore supports describing a return process rather than concealing the inconsistent dates. The original is now conserved by the Biblioteca Nacional de Antropología e Historia, whose digital presentation allows its pages to be studied without equating access with ownership.