This study presents new insights into the effects of halogens (F and Cl) and phosphorous (P) on rare earth element (REE) partitioning between carbonatite and alkaline silicate melts. F, Cl and P are elements that are abundant in carbonatites and alkaline magmatic systems and they are considered to play an important role on the REE behaviour. Nonetheless, their effect on REE partitioning between carbonate and alkaline silicate melts has not yet been constrained. Here we present new experimental data on REE partitioning between carbonate and alkaline silicate melts doped in F, Cl and P, in order to (1) test the Nabyl et al. [2020] REE partitioning model in F-, Cl- and P-rich systems, and (2) identify the possible role of F, Cl and P in carbonate melt REE enrichments during alkaline–carbonatite magma differentiation. The experiments were performed at 850–1050 °C and 0.8 GPa using piston-cylinder devices. Starting materials consisted of carbonatite and phonolite compositions doped in F, Cl and P. The experimental results show that REE partitioning is similar in F-Cl-P-rich and -poor systems. The silicate melt composition and its molecular structure (i.e. SiO contents, the alumina saturation index and the alkali/alkaline-earth element ratio), which have already been identified as controlling REE partitioning in F-, Cl- and P-poor systems, still operate in doped systems. No direct effect of the F, Cl or P melt concentrations on REE partitioning has been identified. We also propose an application to natural systems.