Crustal geochemical signatures in carbonatites may arise from carbon recycling through the mantle or from fluid-mediated interaction with the continental crust. To distinguish igneous from fluid-mediated processes, we experimentally determined rare earth element (REE) partitioning between calcite/melt and apatite/melt at subvolcanic emplacement conditions (1–2 kbar, 750–1000 °C). Our data allow modeling of calcite-apatite (Cc/Ap) partition coefficients (D), representing a new tool to bypass the previously required but largely unknown carbonatite melt composition. Experimentally determined magmatic calcite/apatite REE patterns are flat, as DLaCc/Ap/DLuCc/Ap is ~0.75, and they show a slight U-shape that becomes more pronounced with temperature decreasing from 1000 to 750 °C. Application to texturally well-equilibrated natural Ca-carbonatites and calcite-bearing nephelinites shows that some calcite-apatite pairs follow this pattern and, hence, confirm the magmatic nature of the carbonates. DLaCc/Ap/DLuCc/Ap values of other mineral pairs range from 10–2 to 10–3, which, together with a substantial light REE depletion in the calcite, is interpreted as fluid-mediated light REE removal during secondary calcite recrystallization. Calcite/apatite REE distributions are well suited to evaluate whether a carbonatite mineralogy is primary and magmatic or has been affected by secondary recrystallization. In this sense, our tool provides information about the sample’s primary or secondary nature, which is essential when assigning isotopic crustal signatures (in Ca, C, or Sr) or REE patterns to related geologic processes.

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