This research explores the phosphatization process in the São Pedro and São Paulo Archipelago (SPSPA), located in the Equatorial Atlantic, by analyzing the geochemical interactions between guano coatings and the underlying rocks. The study also examines the geochemical characteristics of the substrates, assessing the behavior of major, minor, trace, and rare earth elements, and determines the degree of weathering degradation of guano crusts, speleothems, peridotites and carbonate sedimentary rocks affected by environmental factors as rain, wind and halmyrolysis. The distribution of chemical elements in water-soluble, adsorbed, acid-extractable/exchangeable, readily acid and reducible, acid oxidizable, and residual phases were investigated. The principal findings of this method show that elevated Na levels are leached in water-soluble fractions, thereby highlighting the occurrence of rapid and active geochemical cycling, which is influenced by seawater. In contrast, in more acidic environments (pH close 4.8 to 2.0), considerable amounts of macroelements like P, Fe, Mg, Al, and Mn are found in association with remaining phases, indicating a slower and more incremental geochemical cycle of mature guano in the input and output systems of these nutrients in the archipelago. The mineralogy, as indicated by the presence of mafic minerals such as olivine, augite, and Cr-spinel, as well as phosphates including fluorapatite, collinsite, and spheniscidite, also supports this finding. The findings underscore the complex interplay between biological activities and geochemical processes, which influence the elemental dynamics in the phosphate-rich rocks of the SPSPA at depth. This study not only enhances our understanding of phosphatization processes but also offers important insights into the sustainable management of marine resources in environmentally sensitive areas. The research underscores the necessity of considering biological and environmental variables when examining geochemical cycles, particularly in regions exhibiting distinctive geological and biological interactions that challenge the prevailing models, such as those identified in the ASPSP.