Abstract Lignocellulosic biomass was submitted to a biological pretreatment prior to a catalytic hydroliquefaction in order to produce biofuel. The biodegradation process was conducted over 3months in a reactor under controlled conditions. During the biodegradation process the organic matter was characterised and its evolution was correlated with physico-chemical parameters. In parallel with the analysis of the lipidic fraction, analytical pyrolysis was used to monitor bacterial activity. The alterations of branched to linear fatty acids ratio and of mono- to diacids ratio were compared when determined by thermochemolysis and observed in the directly extractable lipids. The evolution of the phytol to the corresponding isoprenoic ketone ratio was observed to be dependent on the desorption technique since it decreases using headspace while it increases using pyrolysis. “Humic”/“fulvic acids” ratio, infrared spectroscopy and thermodifferential analysis were used to determine the degree of OM complexification.