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Long and complex sequences of intentional organic rich sediments accumulation known as fumiers can often be found in many caves and rock shelters used for herding activities since the Neolithic to current times in the Mediterranean basin. These are mainly composed of burnt animal dung and vegetal remains and are commonly interpreted as the result of livestock domestic occupations and stabling activities. The repetitive and systematic burning processes that occurred for cleaning these spaces provide different layers with different archaeosedimentary features (facies). Fumier facies imply different pre-burial conditions that may influence bone diagenetic processes. In this work, we study the changes occurring in mineral and organic components of bones included in different facies (reelaborated, burned, unburned) in El Mirador cave fumier using Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FTIR). We have carried out an analysis of 47 bone remains from four different facies [ a , r(m) , tf and v ] from archaeological levels dated from the second half of the 5th until the first half of the 2nd millennia cal B.C. We have used a total of 13 parameters through ATR-FTIR to discriminate facies differences through PCA and Machine Learning techniques. The results show differences in crystallinity, organic, and carbonates content between bone remains recovered from fumier facies. Our results demonstrate that burial environments that occur on fumier deposits affect bone components in different ways. Therefore, fumier facies can be differentiated from each other through the diagenetic parameters provided by bone assemblage, distinguishing those well preserved and, therefore, eligible for other types of analyses (isotopes, proteomics, lipids, etc.). Furthermore, Machine Learning can classify the facies through carbonates indices API, C/C, and BPI. This study is an important step towards understanding the taphonomic processes (formation and reelaboration) that occur in fumier sequence as a result of the multiple livestock activities developed in caves and rock shelters. • The study investigates bone diagenetic processes occurring in fumiers context through ATR-FTIR. • Environments and taphonomic history prior to sedimentation have a great influence on the survivorship of bone remains. • Diagenetic trajectories and fire impact on archaeological bones can be used to distinguish facies in fumier sites. • The use of ML is a potential tool for fumier facies distinction when multiple bone diagenesis variables are included. [ABSTRACT FROM AUTHOR]