Anaerobic digestion (AD) is a feasible biological process that converts the organic matter (OM) contained in wastes into biogas besides a by-product named digestate, which is regularly spread in soils. Frequently, the recalcitrant OM of the substrate (i.e. exogenous OM) highly influences the quality of the digested OM. This fact could impede the identification of the endogenous OM (i.e. microorganisms derived) produced during AD. However, the endogenous OM could also impact the OM stabilization processes and therefore, the digestates land use. Recently, the biochemical fractionation method combined with 3D fluorescence has been successfully used to describe the OM quality based on the OM accessibility and complexity [1]. Moreover, fluorescence has shown great potential for monitoring soluble microbial products during microbial growth/decay [2]. Nonetheless, the link between the above-mentioned characterization method with the particulate OM (POM) composition has not been performed before. With that purpose, Fourier transform infrared combined with a photoacoustic detector (FTIR-PAS) is a promising approach to characterize the POM of many organic wastes [3]. This research aims to evaluate the impact of totally biodegradable and partially biodegradable substrates on the OM quality and soluble compounds identification during AD. Additionally, the influence of a starvation period on the OM composition has been evaluated.