Pyrochlore-supergroup minerals containing relatively high Si concentration are quite common in various geochemical parageneses, e.g., carbonatites, alkaline syenites, pegmatites. However, the role of Si and the mechanism of its incorporation into the structure of these minerals, although widely discussed, have not been explained definitively. Our paper reports the results of comprehensive SEM, EPMA, XRD, TEM, and MAS-NMR studies performed for the first time on a natural pyrochlore, which is the late-magmatic to early hydrothermal accessory component of the nepheline syenite in the alkaline Mariupol massif in Ukraine. It represents partly metamict, patchy-zoned, A-cation depleted, REE-, U-, and Th-bearing fluornatropyrochlore, locally exceptionally rich in SiO2 (up to 13.01 wt%) that underwent both primary and secondary alterations, leading to kenopyrochlore or hydropyrochlore species. The primary alteration was induced by high-temperature, Ca2+- and Si4+-rich, and F− moderate fluids, which affected only some domains of the pyrochlore crystals and resulted in filling the A site vacancies mainly by Ca2+, but also Mn2+, Sr2+, and K+. The secondary alteration, induced by the exposure of the host rock to ground water driving fluid-mediated coupled dissolution-reprecipitation process, affected the whole pyrochlore crystals (both Si-enriched and Si-free domains) and caused, among others, the leaching of some A- and Y-site components. TEM investigations indicate that the selected-area electron diffraction patterns taken from Si-poor areas show strong and sharp diffraction spots related to well-crystalline pyrochlore, whereas the Si-rich areas show weaker spots with a diffuse diffraction halo that are typical of metamict material. Due to the fact that no intergrowth with other Si-bearing phases was observed in the TEM images even at very high magnification, it might be concluded that Si4+ can occupy severely α-decay damaged and chemically altered portions of this structure. The absence of Si in the sixfold-coordinated B site has been corroborated both by compositional relationships, and by the lack of any Si4+ signal around −200 ppm in the MAS-NMR spectrum. A broad signal in the spectrum appearing at around −84 ppm, points to an amorphous species with tetrahedrally coordinated Si, close to Q(2) species defined as Si atom with two bridging O atoms, i.e., [Si(OSi)2(−)2], in the form of finite-length chain-like structures, located in the damaged A and B sites of the primary structure.