Abstract The Martian meteorite ALH84001 preserves evidence of interaction with aqueous fluids while on Mars in the form of microscopic carbonate disks. These carbonate disks are believed to have precipitated 3.9 Ga ago at beginning of the Noachian epoch on Mars during which both the oldest extant Martian surfaces were formed, and perhaps the earliest global oceans. Intimately associated within and throughout these carbonate disks are nanocrystal magnetites (Fe 3O 4) with unusual chemical and physical properties, whose origins have become the source of considerable debate. One group of hypotheses argues that these magnetites are the product of partial thermal decomposition of the host carbonate. Alternatively, the origins of magnetite and carbonate may be unrelated; that is, from the perspective of the carbonate the magnetite is allochthonous. For example, the magnetites might have already been present in the aqueous fluids from which the carbonates were believed to have been deposited. We have sought to resolve between these hypotheses through the detailed characterization of the compositional and structural relationships of the carbonate disks and associated magnetites with the orthopyroxene matrix in which they are embedded. Extensive use of focused ion beam milling techniques has been utilized for sample preparation. We then compared our observations with those from experimental thermal decomposition studies of sideritic carbonates under a range of plausible geological heating scenarios. We conclude that the vast majority of the nanocrystal magnetites present in the carbonate disks could not have formed by any of the currently proposed thermal decomposition scenarios. Instead, we find there is considerable evidence in support of an alternative allochthonous origin for the magnetite unrelated to any shock or thermal processing of the carbonates.