Intracrystalline alteration is present in approximately 25% of the low-Mg calcite cement throughout the lowermost 160 m of the Middle to Upper Devonian Pillara Formation in the Emanuel Range, Canning Basin, Western Australia. A younger, luminescently and chemically distinct calcite phase disrupts primary zonation in older cement and results in irregular, mottled cathodoluminescence (CL). The younger calcite is always in optical continuity with host calcite. Continuous records of Mg, Fe, Mn, and Sr abundances were measured across concentrically zoned, non-CL and yellow-CL cement altered by orange-CL calcite using a new microprobe method designed for high spatial resolution and rapid collection of minor-element abundances in calcite cement. Minor-element composition of the crosscutting, orange-CL phase, designated as cement VIII, differs significantly from that of the older, zoned cement, designated as cement VIa. Mg abundance in cement VIa is variable, ranging from 700 to 4600 ppm, with a mean of 2760 ppm, whereas that of cement VIII is relatively constant at about 400 ppm. Mn in the yellow-CL zones of cement VIa is variable, 400-7720 ppm, with a mean of 4025 ppm. Mn in cement VIII is relatively constant at 1420 ppm. Fe and Sr were not detected in cement VIa. Abundances of Fe and Sr are highly variable in cement VIII. Fe ranges from < 45 ppm (detection limit) to 2425 ppm, with an average of 1025 ppm. Sr abundance is generally < 330 ppm (detection limit) but reaches maximum values of about 500 ppm. Low-Mg calcite traditionally is regarded as a stable carbonate phase with little tendency toward intracrystalline alteration of chemistry or microstructure. Significant elemental variations measured over small-scale intervals within time-equivalent zones in cement VIa indicate that some parts of the crystal have different chemical potential, which could provide the thermodynamic drive for intracrystalline alteration. Alteration could take place either by a one-step, iterative process of recrystallization or by a two-step, dissolution-cementation process. Lack of micro-collapse features in host calcite, in combination with lack of minor-element memory between host and secondary calcite, support alteration by recrystallization at a high water-rock ratio. However, most alteration of cement in the Emanuel Range probably originated by dissolution-cementation, on the basis of the combination of: (1) lack of minor-element memory effect between host and secondary calcite, and (2) rare occurrences of concentrically zoned secondary calcite in which the zonation is parallel to the contact with the host cement. Creation of intracrystalline porosity by partial dissolution of metastable parts of low-Mg calcite could provide conduits for fluid and element transport that have been unrecognized in modeling porosity changes and fluid movement through carbonate strata.