X-ray fluorescence (XRF) core scanning has become widely available for geological studies during the last decade. The data obtained from XRF core scanning, however, may be strongly influenced by the amount of organic matter, water content, density and porosity of the sediment matrix. In this study we discuss the usefulness of XRF core scanning to distinguish different kinds of organic-rich sediments and peat based on examples from tropical Lakes Kumphawapi and Nong Leng Sai in Thailand. We examined how sedimentary factors influence XRF core scanning analyses by comparing elemental and scattering ratios to lithological changes and quantitative LOI, TOC, biogenic silica (BSi) and grain-size values. Our comparison suggests that the (inc/coh) scattering ratio is of limited use as an indicator for variations in LOI and TOC in peaty gyttja or peat. In Lake Kumphawapi's sediments, Si/Ti ratios reflect clastic input associated with grain-size variations rather than BSi contents. The Ti-normalized ratios of Si, Zr, Sr, K and Rb are linked to mineral input and associated grain-size variations. We conclude that XRF core scanning of organic-rich tropical lake sediments and peat is useful to infer palaeoenvironmental conditions. However, XRF core scanning data does not stand-alone and needs to be underpinned by additional proxies.