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Fast development of centralized agricultural biogas plants leads to high amounts of digestate production. The treatment and disposal of liquid fractions after on-site digestate solid–liquid separation remains problematic due to their high organic, nutrient and aromatic contents. This work aims to study the variability of the remaining compounds in the digestate liquid fractions in relation to substrate origin, process parameters and solid–liquid separation techniques. Twenty-nine digestates from full-scale codigestion biogas plants and one waste activated sludge (WAS) digestate were collected and characterized. This study highlighted the combined effect of the solid–liquid separation process and the anaerobic digestion feedstock on the characteristics of liquid fractions of digestates. Two major clusters were found: (1) liquid fractions from high efficiency separation process equipment (e.g., centrifuge and others with addition of coagulant, flocculent or polymer) and (2) liquid fractions from low efficiency separation processes (e.g., screw press, vibrating screen and rotary drum), in this latter case, the concentration of chemical oxygen demand (COD) was associated with the proportion of cow manure and energy crops at biogas plant input. Finally, SUVA254, an indicator for aromatic molecule content and the stabilization of organic matter, was associated with the hydraulic retention time (HRT).