Carbonatites and their comagmatic silicate rocks related deposit provide significant resources of rare earth elements (REEs), niobium (Nb) and other elements such as U, Th, Mo, V, Ba, Sr, etc. However, the genesis of mineralization, especially for REEs and Nb, in carbonatite remains enigmatic. Previous liquid immiscibility experiments have demonstrated that both REEs and Nb are preferentially enriched in the silicate conjugate instead of carbonate melts under anhydrous conditions. Nevertheless, ligands other than carbonate ion appear to be abundant due to ubiquity of apatite, baryte, celestine, fluorite and sodalite in carbonate–silicate magmatic systems. Here, we experimentally investigate the trace element partitioning between natrocarbonate and silicate (nephelinite) melts in systems doped with varying amounts of additional F−, PO43−, Cl−, and SO42− ligands (0, 2, 4 and 6 wt%) to understand and constrain the role of ligands.The experiments were conducted at 850 °C and 0.1 GPa using rapid quench cold-seal pressure vessels (CSPVs). A comparison of experimental partition coefficients in this study reveals that the significant amounts F− and PO43− incorporated in the silicate melts can increase the D values for REE by influencing melt structure (DLaCM/SM = 0.85–7.42). In contrast, irrespective of the amount of added Cl− and SO42−, DCM/SM is not affected significantly by these species and the DREECM/SM values remain always lower than 1 (DLaCM/SM = 0.12–0.40). Notably, the DNbCM/SM values are all <1, with only one exception containing 6 wt% F. Besides, in all the investigated systems, Ba, Sr, Mo, V, Cs, Rb and Li preferentially partition into the conjugate carbonate melt. All the high field strength elements (Pb, Th, U, Zr, Hf, Nb, Ta), transition metals (Mn, Co, Cu, Zn) and common network formers (Ga, Ge) essentially partition into the silicate melt.