Prehistoric shell middens, called "sambaquis", occur along the Brazilian coast, but their geoarchaeological and pedological contexts remain little explored. We characterized micromorphological attributes and forms of phosphate of key horizons of a soil at Sambaqui. We identified how pedogenesis may affect archaeological materials, helping interpretations relating to the occurrence of elevated concentrations of phosphate, associated with habitation. Micromorphology and microchemical analysis using SEM/EDS investigated well-studied horizons of these shell midden soils. Phosphate mobility is demonstrated by the occurrence of secondary Ca-phosphates in deeper strata free from artifacts, below the midden. Ca-apatite forms well-defined microaggregates of illuvial/chemical origin. The primary sources of the Ca and P have disappeared, and we suggest they were organic materials and ash rather than the existing fragments of bone apatite or shells present in the overlying archaeoanthrosol. The in situ preservation of denser and larger bone fragments may be attributed to the apatite-rich micromass, which retards Ca-apatite dissolution from bone fragments. The presence of phosphate-rich lower strata without direct anthropic inputs indicates that P leaching and precipitation as secondary forms has occurred during wet climate episodes. © 2013 Elsevier Ltd and INQUA.