The chemical, physical and palaeobotanical composition of peat can be used to infer the history of a peatland and the processes presently operating within it. Here we present new data on the geochemistry of a peat sequence from a lowland palm swamp, Quistococha, in Peruvian Amazonia. We show, through comparison with subfossil pollen data from the same sequence, that changes in the depositional environment cause changes in peat properties including lignin content, C/N ratios, and the abundance of several metal cations, but that these properties are altered by post-depositional processes to a large extent. An upward trend in the top 1.5 m of the sequence in the concentrations of N, K, Ca, Mg and Na probably reflects nutrient uptake and cycling by the standing biomass. Upward trends in Mn and Fe concentrations suggest that limited oxygenation of the peat may occur to a similar depth. Comparison with other published records suggests that such deep biological alteration may be characteristic of tropical forested peats.