Here, we report the first occurrence of two (Ca-Y)-phosphate phases in apatite crystals from ancient rocks from both the Barberton greenstone belt and the Pilbara Craton. First, a cubic Ca3Y(PO4)3 phase was observed in a sample of silicified tuff from the Mendon Formation from the Barberton greenstone belt. A second phase, corresponding to a synthetic compound with the formula CaYP7O20, was observed in a sample of black banded chert from the Hooggenoeg Formation of the Onverwacht Group and in a sample of chert from the Strelley Pool Chert Formation (East Pilbara Terrane). Based on the presence of these phosphates and specific textures revealed by transmission electron microscopy, we argue for the importance of dissolution-reprecipitation processes in the formation of these phosphate phases. Temperature was likely not the primary parameter controlling the crystallization of the Ca3Y(PO4)3 and CaYP7O20 phases. Instead, the REE-F complexes in an H2O solution and the specific budget of REEs and Y in apatite were likely responsible for the nucleation and formation of the (Ca-Y)-phosphate phases in the Archean rocks of the Barberton greenstone belt and Pilbara Craton.