Carbonatites are fascinating magmatic rocks because of their anomalous compositions, including the fact that some of these rocks host major rare earth element (REE) deposits. Despite much recent work, our understanding of their genesis and the composition of initial carbonatite melts is hindered by two major obstacles: most carbonatites we see are intrusive rocks, and they are commonly affected by metasomatic overprint. Here, we report experimental data in which we use apatite as a geochemical proxy to see back through crystallization and metasomatic events, thus making it possible to decipher the composition of carbonatite melts. We determined partition coefficients between apatite and carbonatite melts for a broad range of elements. The Na-rich nature of carbonatite melts plays an important role in apatite-melt partition coefficients, which are in the range of 1–7 for Sr, Y and REE in carbonatite systems. Using our new experimental data combined with >700 apatite composition data from carbonatites in various geodynamic settings, we show that carbonatite melt REE contents vary by more than two orders of magnitude. This variation cannot be solely produced by crystal-melt fractionation, implying that some carbonatite melts must be REE-rich or REE-poor initially, and that they mostly remain so during differentiation. We conclude that the degree of REE enrichment reflects carbonatite melts produced by immiscibility from variably differentiated alkaline magmas.