Changes in organic matter concentration in sediment cores from natural archives such as lakes and wetlands can be a valuable tool in paleoenvironmental studies. The molybdenum incoherent: coherent scattering ratio (moly ratio) from the Itrax core scanner offers the potential to measure down core changes in sediment organic content. The analysis is rapid, high resolution and does not destroy samples. We built upon previous studies of the power and potential pitfalls of using the moly ratio as a proxy for organic content in sediments. An important difference between our study and previous work is that we accounted for the total mass of moisture and organic content in the sediment using loss on ignition. This had the advantage over total organic carbon measurement of being able to account for all light elements (H, C, N, and O) that would affect the moly ratio. We used redundancy analysis to determine that both organic and moisture content can have large, independent, and variable effects on the moly ratio. It is therefore critical that moisture and organic content have a constant relationship with each other in a core. Samples with higher moisture to organic content ratios can over predict organic content and vice versa. The effect of moisture only accounted for 30% of the prediction error for the moly ratio in our study. We argue that a large part of remaining error reflects sample heterogeneity. XRF core scanning and organic content determination from sub-samples can show different results because the mean sediment composition is different. We recommend that calibration sub-samples are large (≥2 cm3) in potentially heterogeneous sediments, authors should report the sample size used for calibration purposes, and multiple scans of the core may be needed. If organic content is an important proxy for an environmental reconstruction, we recommend calibration of the moly ratio and confirming a constant relationship between moisture and organic content. Thoughtful selection of sub-samples for this purpose could mean that calibration can be performed with a minimum of extra effort.