Reflectance composites that capture bare soil pixels from multispectral image data are increasingly being analysed to model soil constituents such as soil organic carbon. These temporal composites are used instead of single-date multispectral images to account for the frequent vegetation cover of soils and, thus, to get broader spatial coverage of bare soil pixels. Most soil compositing techniques require thresholds derived from spectral indices such as the Normalised Difference Vegetation Index (NDVI) and the Normalised Burn Ratio 2 (NBR2) to separate bare soils from all other land cover types. However, the threshold derivation is handled based on expert knowledge of a specific area, statistical percentile definitions or in situ data. For operational processors, such site-specific and partly manual strategies are not applicable. There is a need for a more generic solution to derive thresholds for large-scale processing without manual intervention. This study presents a novel HIstogram SEparation Threshold (HISET) methodology deriving spectral index thresholds and testing them for a Sentinel-2 temporal data stack. The technique is spectral index-independent, data-driven and can be evaluated based on a quality score. We tested HISET for building six soil reflectance composites (SRC) using NDVI, NBR2 and a new index combining the NDVI and a short-wave infrared (SWIR) band (PV+IR2). A comprehensive analysis of the spectral and spatial performance and accuracy of the resulting SRCs proves the flexibility and validity of HISET. Disturbance effects such as spectral confusion of bare soils with non-photosynthetic-active vegetation (NPV) could be reduced by choosing grassland and crops as input LC for HISET. The NBR2-based SRC spectra showed the highest similarity with LUCAS spectra, the broadest spatial coverage of bare soil pixels and the least number of valid observations per pixel. The spatial coverage of bare soil pixels is validated against the database of the Integrated Administration and Control System (IACS) of the European Commission. Validation results show that PV+IR2-based SRCs outperform the other two indices, especially in spectrally mixed areas of bare soil, photosynthetic-active vegetation and NPV. The NDVI-based SRCs showed the lowest confidence values (95%) in all bands. In the future, HISET shall be tested in other areas with different environmental conditions and LC characteristics to evaluate if the findings of this study are also valid.