Alkaline igneous rocks are one of the most important sources of rare earth elements (REE) worldwide, due to their elevated contents of HFSE (e.g. Zr, Nb, REE), in particular the heavy rare earth elements. This study presents detailed geochemical and geochronological characteristics of a REE-bearing mineral assemblage forming Zr–REE–Nb mineralisation in nepheline syenite dykes at the contact zone of the Čistá granodiorite pluton (Czech Republic). The primary REE-bearing accessory minerals, monazite-(Ce), pyrochlore, fergusonite-(Y) and gadolinite-(Ce), underwent multiple alteration driven by hydrothermal fluids. Fine-scale investigation of the alteration assemblages, using a combination of electron probe microanalysis (EPMA), transmission electron microscopy (TEM), and laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS), revealed the occurrence of two main stages of alteration and provided insights into the relationships among the primary and secondary REE-bearing minerals and the replacement mechanisms. The first alteration stage took place when the pluton cooled below 600°C. This was marked by monazite-(Ce) breakdown and its replacement by allanite-(Ce) and fluorcalciobritholite-(Ce), as well as alteration of primary pyrochlore and the formation of U-rich oxide inclusions. The second alteration stage involved alkali-fluid-induced metasomatism at ∼200–450°C, affecting the majority of the REE-bearing assemblage and leading to the formation of new secondary minerals such as bastnäsite-(Ce), britholite-(Ce) and gadolinite-(Y), and a second generation of pyrochlore. Age determination of primary monazite-(Ce) yielded a lower intercept U–Pb age of 376.5 ± 9.9 Ma, consistent with mean 208Pb/232Th age of 375 ± 3.2 Ma, which constrains the timing of the late magmatic hydrothermal processes related to the main magmatic event in the Čistá pluton. This study provides new insights into stability relations of REE-bearing accessory minerals in an alkali-rich environment. It also highlights the advantages of using comprehensive analytical methods from microscale to submicron-scale as a fundamental approach in the petrochronological investigation of metasomatic processes.